Prosecutors in the far western Xinjiang region filed the motion with a court in the city of Urumqi, according to their official account on Sina Weibo, a Chinese equivalent of Twitter.
Prosecutors said they "instituted proceedings at the Urumqi Intermediate People's Court against defendant Ilham Tohti who is suspected of separatism".
Chinese police detained the outspoken economics professor in January. His detention has prompted condemnation from the US, EU and international rights groups.
Tohti's lawyer Li Fangping could not immediately be reached for comment today.
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The move to file charges against him comes as China is engaged in a crackdown over a series of violent attacks that Beijing blames on religious extremists and "terrorists" seeking independence for the region.
Such violence has grown more frequent over the last year and has even spilled outside the vast resource-rich region.
Beijing has blamed militants from Xinjiang for an attack in Urumqi which killed 31 people in May, and for a March stabbing spree at a train station in the southwestern city of Kunming in which 29 people died.
The US State Department and the EU have both condemned Tohti's detainment. Human rights group Amnesty International has called for his release.
In June, attorney Li told AFP that Tohti was denied food for a period of 10 days in March during which he was given a single glass of water.