There are several obvious differences between the poems: Kubla Khan is a fragment, whereas The Rime of the Ancient Mariner is a fully realized piece, to name one difference. The Rime has a well developed central theme—the Mariner's sin in killing the albatross and the moral ramifications of that act—which Kubla Khan lacks.

In formal terms, Kubla Khan is much more inventive and organic in meter and rhyme scheme than the Rime, which sticks primarily to quatrains with an abcb rhyme. Kubla Khan does not follow any obvious rhyming pattern, and its meter is famously indeterminate. What both poems share, however, is an innate musicality that is in harmony with their subject matter.

While both poems include striking images of nature, the Rime has a more developed symbolic structure than Kubla Khan. The Mariner's voyage is a kind of Christian allegory of sin and redemption, while at the same time a meditation of the moral import of the natural world. Kubla Khan, while including some of the most striking images in English poetry, is not allegorical in the same sense; instead, it deals more generally with the difference between the power of nature and the power of man.