Rev. Frank Schaefer's congregation in Lebanon County held a vigil in support of the pastor on Sunday.
Schaefer, 51, could be suspended, reprimanded or lose his credentials because he performed a wedding ceremony for his son in 2007 in Massachusetts.
He had informed his superiors about it beforehand and did not face any consequences until April, when a congregant filed a complaint.
Methodist ministers are not allowed to perform same-sex marriages or civil unions.
Schaefer said nothing was more important to him than supporting his son, who he said had struggled with embracing his own sexual orientation.
"Had I said no to my son's request, that would have negated every affirmation that we gave him over all these years," he said.
The United Methodist Church formally accepts gay and lesbian members but teaches that homosexuality is not compatible with Christian teaching.
Schaefer's trial will begin Nov. 18 at a Methodist retreat in Spring City, about 35 miles northwest of Philadelphia.
He could avoid trial by agreeing not to perform another same-sex marriage, but he has decided not to do that.
Three of his four children are gay.
The Associated Press contributed to this report.