The 58-year-old American legend also included Ilie Nastase in his blast after the Romanian recently made derogatory remarks over women and Serena Williams's unborn baby.
Court, the winner of a record 24 Grand Slam titles, has made a string of lurid claims over same-sex marriage, homosexuality and transgender children.
"Margaret Court and Ilie Nastase have taken tennis back to the dark ages," McEnroe said in a Eurosport video.
"So I pronounce you man and wife."
McEnroe suggested a solution to the ongoing push to have the Margaret Court Arena at the Australian Open renamed in protest at the 74-year-old's views.
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"But when same-sex marriage becomes legal in Australia, I will call my good friend Elton John to host the biggest same- sex marriage ceremony ever seen -- in the Margaret Court Arena."
McEnroe added that he was a firm supporter of same-sex marriage.
"I don't see any reason for them not to be as miserable as everyone else," he joked.