Beijing accused Ursula Gauthier, the China correspondent for France's L'Obs news magazine, of supporting terrorism after she wrote an article questioning official comparisons between global Islamist violence and the unrest in the homeland of the Uighur ethnic minority.
It then refused to renew her credentials, obliging her to leave when her visa expires.
Speaking from her Beijing home before leaving for the airport, Gauthier said that the future looked bleak for journalists in China.
"This could be really dangerous in the future."
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France and Europe should be "concerned about what is going on here, not because it is a journalist, not only because of the freedom of press, but also because it is about China and what China is doing to its minorities, and even its majority, the problem is the same," she added.
Gauthier had told AFP earlier that she felt "a very strong feeling of surreality" on her last day in Beijing, as she carried out her final packing and finished an article ahead of a late-night flight out of the country.
In her story for L'Obs, Gauthier questioned China's motives in expressing sympathy for the victims of the November 13 Paris attacks, writing that they were calculated to tie Beijing's harsh policies in Xinjiang into the fight against global terrorism.
The veteran reporter, who has spent years in China, suggested that violence by Uighurs against civilians in the region -- where clashes have killed hundreds in recent years -- was in part driven by resentment of government policies.
"I didn't write that I supported terrorism, I never supported terrorism in my article," she told AFP earlier.
Gauthier views her treatment as an attempt "to intimidate foreign correspondents in China, particularly on issues concerning minorities, especially in Tibet and Xinjiang".
Chinese media and officials heavily criticised her article, with the Communist Party-affiliated Global Times saying it "severely distorted the reality in Xinjiang" and represented a "double standard" on terrorism.
The journalist said her home address was posted online alongside death threats from angry readers.
Asked whether Gauthier would ever be allowed to return to China, ministry spokesman Lu Kang left the issue open on Thursday, telling a regular briefing: "It entirely depends on her.