Since 2003, the "Zhongmu Wang" website, or 2muslim.Com, functioned as an "online network of Muslims sharing Islam", according to archived descriptions.
But today the site was inaccessible, showing only a message stating it was "under maintenance".
Two of its affiliated social media accounts were also unavailable, displaying messages that declared one account "abnormal" and the other "in violation of required guidelines".
China officially has more than 23 million Muslims, though some independent estimates say there may be as many as 50 million -- which would put China among the world's top 10 Muslim nations.
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The closure came after the posting of an open letter to Xi calling for a halt to the "brutal suppression" of activists and the immediate release of those still detained by the state, according to students who wrote the petition.
The letter criticised Xi for overseeing a crackdown on dissent since coming to power in 2012, with hundreds of lawyers, activists and academics detained and dozens jailed.
"You are not responsible for all of the crimes of the totalitarian system, but as the totalitarian system's head and its commander-in-chief of repression, you must take responsibility for the blood and tears which now flow," it said.
Yi Sulaiman Gu, a Muslim student studying in the US at the University of Georgia, told AFP the website shut the day after he posted the letter to a forum that had previously hosted sensitive discussions on issues such as China's persecution of Muslim dissidents.
"We believed it would be safe for Zhongmu to post it there," Gu said.
Phone calls to the website's owner went unanswered.
But the letter gained attention when screenshots of it were reposted to China's Twitter-like Weibo by opinion leader Xi Wuyi, a professor of Marxism at the Chinese Academy of Social Sciences, who said it proved the site supported Xinjiang separatists.
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