Wujie News website in March published an anonymous letter accusing the Chinese leader of a litany of policy mistakes and asking him to step down for the good of the country on the eve of a high-profile political meeting.
The letter, signed "Loyal Communist Party members," was quickly deleted and staff reported a wave of detentions as authorities tried to track down the document's author.
Media criticism of top leaders is almost unheard of in China, where the press is strictly controlled.
Wujie chief executive officer Ouyang Hongliang and senior editor Cheng Shengzhong have been "out of contact" for 101 days "assisting relevent departments with an investigation", Ouyang's wife Liu Yankun said in a letter posted on social media.
She said the news outlet had been "forcibly closed" in March, and that many staff had their benefits such as medical insurance suddenly cut.
"We are suffering from fear and worry," Liu said, adding she had only been able to speak with her husband "a few times" by telephone.
One former reporter at the outlet who asked not to be named said managing editor Huang Zhijie was detained in March but later released.
Beijing freelance journalist Jia Jia also went missing shortly after the letter was published, and authorities rounded up the relatives of several dissidents living abroad.
Xi has tightened already strict controls on the media since coming to power in 2012, and this year urged state-run outlets to "reflect the will of the party".
He has presided over a slowdown in economic growth and a clampdown on civil society that has seen hundreds of people arrested.
The letter, seen by AFP in a cached form, berated him for centralising authority, mishandling the economy and tightening ideological controls.
Beijing-based Wujie -- known as "Watching" in English -- was founded in 2015 with funding from the provincial government of Xinjiang in China's northwest.