Tom Bombadil's origins in the cosmology of Middle-earth have puzzled even erudite fans, as he is arguably the only character in Tolkien's entire legendarium who does not neatly fit into any of the categories of beings Tolkien created. Speculative ideas about his true nature range from simply a wise Elven hermit to an angelic being (a Maia or Vala), to the creator, that is, God, who is called Eru Ilúvatar in J. R. R. Tolkien's legendarium. Tolkien explicitly denied this last possibility.
The most popular theory is that Bombadil is a Maia, as Tom seems to have unlimited supernatural power inside the boundaries that he set for himself, and perhaps the reason why he has such powers is the fact that he is content to live within these limits. "Eldest, that's what I am ... Tom remembers the first raindrop and the first acorn ... He knew the dark under the stars when it was fearless before the Dark Lord came from Outside." The Dark Lord Bombadil refers to is probably Melkor and not Sauron. But in that case, Tom was already there even before the Valar entered the world, dismissing the theory that he is a Maia. Another argument against the Maia theory is his immunity to the corrupting power of the One Ring, whereas both Saruman and Gandalf, both Maiar, were clearly not immune. In addition, he is eager to protect the Hobbits from danger within his own domain, yet is completely indifferent to the threat to Middle Earth as a whole, which is paradoxical and also uncharacteristic of a Maia.
Bombadil could be part of the Music of the Ainur and that would explain why he was there in the beginning, but if he was indeed part of the music, it is not said why he exists. Everything in the music had a purpose, and Bombadil's is not explained.
Other possibilities (compatible with the above theory) are that he is an abstract, a concept: possibly the embodiment of Arda itself, a "Father Nature," or some kind of 'spirit' that (unlike the Maiar) was of non-divine nature. Not only does the Ring have no effect on him, Tom himself seems unable to affect the Ring in return which shows that Tom was outside the divine plan and struggle and had no position in it.
Another possibility for Tom Bombadil's nature arises from careful reading of the Ainulindalë, when Eru Ilúvatar proclaims, "Let these things Be! And I will send forth into the Void the Flame Imperishable, and it shall be at the heart of the world, and the World shall Be." It is a possibility that Tom Bombadil is some sort of guardian or protector of the Imperishable Flame. If one considers Bombadil's constant reference to "water, wood, and hill," three common motifs Tolkien uses to describe Middle Earth, it is possible to see how Bombadil is an encapsulation of Arda as it should be. There is substantial debate among those who choose this view regarding the exact nature of the Flame itself, yet it is another possibility that must be considered.
Gandalf calls Tom Bombadil the eldest being in existence; this is also evident by his Sindarin name Iarwain Ben-adar (Eldest and Fatherless). Dwarves called him Forn, Men Orald. All these names apparently mean "Eldest." However, Fangorn (Treebeard) calls himself the eldest living being of Middle-earth and that he was there before anyone else. Bombadil is just called the 'eldest.' If Tom Bombadil is indeed not a normal being but rather a supernatural being or "concept" this is, however, not necessarily a contradiction (Treebeard is likely the oldest living being, while Bombadil could be an older supernatural being). Concerning Fangorn, Tolkien remarked: "Fangorn is a character in my story and even he does not know everything." Tom Bombadil was almost certainly created to be an enigma.
In reference to Bombadil, Tolkien himself said that some things should remain mysterious in any narrative, hidden even to its inventor. He also placed the fate of the Entwives in this category, as well as the Cats of Queen Berúthiel, although hints of the latter story have emerged in posthumously released materials.
It is clear, though, that Bombadil was not, in Tolkien's conception, part of Middle-earth from the start. He was invented in honour of his children's Dutch doll, about whom Tolkien would invent stories. These predate the writing of The Lord of the Rings. Tom Bombadil was, however, part of The Lord of the Rings from the earliest drafts.
It is possible that Tolkien's reference to "the Doom of Man" being hidden to the minds of the Valar hint at Tom's true identity. It should be noted that none of the characters in The Lord of the Rings could know of Iluvatar's (God's) plans for mankind's fate after death. However, Tolkien, as a devout Christian, believed that man's fate was salvation at the hands of the Son of God.
Similar to the hidden doom of man, Tom Bombadil may be a reference of things that occur after the end of the events of the The Lord of the Rings, during the age of man and the entrance of Christianity. He is a player completely outside the events of The Lord of the Rings, awaiting, perhaps, the fruition of Iluvatar's final creation song. It may be that Bombadil is a manifestation of Christ Himself. However, most serious scholars refute this assertion, as the presence of Christ before the historicity of his appearance does not mesh well with Tolkien's very seriously-held Catholic views.