In the Channel Islands the upkeep of churches is paid for through Parish Rates, which everyone has to pay.
But Leo Thomas said he finds it "extremely questionable" he should pay for a church that "openly discriminates against the gay community".
The Anglican Dean of Guernsey said he would respond to Mr Thomas privately.
More on the church rates story, and other news
Mr Thomas wrote the open letter to ask to be removed from paying church rates "due to the Church of England's institutional homophobic stance on gay marriage".
He wrote: "As a person classed as a sinner and not worthy to get married in a church why should I be obliged and forced to pay a penny towards the costs of said church?
"If the Church of England was a private company, I probably would have a strong case of discrimination in court."
He said this year he would donate the Â£7.94 he paid for his 2016 church rates to a local charity instead.
The central government on the island is the States of Guernsey, but each parish also has its own douzaine.
Parish Rates, separated in owner and refuse rates, are charged to cover the cost of services provided by the douzaine, which are determined by the value of the owner's property, similar to Council Tax.
Services provided include rubbish and recycling collection, licensing, boat moorings, highways, planning permission and the upkeep of parish churches.
Both the Anglican Dean of Guernsey the Very Reverend Tim Barker, and the constables of St Andrew's Parish, where Mr Thomas lives, have declined to comment.
Same-sex marriage in Guernsey was approved in December but the law has not yet come into effect, but is expected to this summer.
Deputy Peter Ferbrache said he is against any form of discrimination and sympathises with Mr Thomas, but said he disagrees with withholding rates contributions.
"I regard the church buildings as an important part of our heritage. They should be preserved. "
A gay man from Guernsey has refused to pay for the upkeep of his parish church because of its "homophobic stance on gay marriage".