My thoughts are in blue, words to delete are in red, suggested rephrasing is in orange.

I am writing to seek representation for my 125,000- word epic fantasy novel, Photomancer. It follows two young men hosting ancient spirits, one destined to save the world, the other to break it- and both of them in love with each other in a world where such things are punishable by death. You might think of it as N.K. Jemisin’s The Hundred Thousand Kingdoms meets Book of the Ancestor by Mark Lawrence. This is a great intro. The only tweak I have is that there is an echo with the word world that needs addressed. Your word count is a bit high, if you're able to trim it, that won't hurt you, although there is wiggle room for world building with fantasy.

Yoon is a thriving world. Magic is a rare, useful, dangerous gift that leaves physical scars on its users unless they belong to the Thyman Church. Thyme is Yoon’s superpower, I don't know what this means. What is thyme? And can a world have a superpower? with a bustling economy and an impeccable military- but with a Church that beheads anyone who doesn’t think like them and burns anyone with Scars.

Kohnui is chosen against his wish to train at the Thyman Conservatory of magic- as is Cameron, son of the richest noble in the land. But Kohnui is hiding a terrible secret, and he must constantly battle his attraction to Cameron while struggling to hide his Scar during his training at a school full of the very people that would kill him if he were ever discovered. Yet Cameron has his own secrets and his own past, as Kohnui will soon discover; and their seemingly insignificant struggles might be the turning point in a heavenly war going back thousands of years, with the fate of both the heavens and Yoon hanging in the balance. I don't really know what that means. You need to be more clear about the plot, and what the conflict is. Right now we've got secrets and unrequited / star-crossed love, but that's a story that's been told a million times. What's different about yours? What about those ancient spirits? Why does the fate of the entire world hang on these two?

Photomancer is my first full-length novel, but I have published several short stories in local magazines and anthologies, including one which won the CREPLA award (a regional sub-Saharan African prize). I have worked as a junior editor for faculty magazines.

I understand you are always on the lookout for fresh talent, and I would be thrilled to count myself among the ranks of your clients. I gather you enjoy fantasy with strong voices and character-driven stories that shed a spotlight on Latinx and other underrepresented groups, and I think this is something in my work that would particularly appeal to you. Thank you very much for your consideration.

Overall, nicely done with a good bio. You just need to get more plot in there, as the big points you're hitting (unrequited love, star-crossed love, secrets, magic school, etc) have all been done before. Get more of what makes this story distinct - particulary the plot - into the query.