Tests showed the 49-year-old man, from Nanchong in the southwestern province of Sichuan, had contracted the virus, the official Xinhua news agency said late Tuesday citing local health authorities.
The patient had been exposed to dead poultry and was initially diagnosed as having pneumonia, the report said, adding that authorities said people who had had close contact with him have shown no symptoms.
Experts believe the infection is an individual case and the risk of further infection is low, it said.
ProMED-mail, a reporting system run by the US-based International Society for Infectious Diseases, said on its website: "To the best of our knowledge, this is the 1st human case of H5N6."
The strain has been used for a vaccine in poultry, and it has been identified in migratory birds in Taiwan, it added.
According to Taiwan's Centers for Disease Control, H5N6 has previously been detected in the environment in Germany, Sweden and the US.
Bird flu has taken a significant toll in China this year, with a total of 250 cases and 96 deaths from the H7N9 strain in the January-March period, according to the National Health and Family Planning Commission.
Last year the country recorded 46 deaths and 144 cases from the H7N9 outbreak, which started early in 2013 and returned in the autumn.
The virus ignited fears that it could possibly mutate to become easily transmissible between people, which might threaten to trigger a global pandemic.
But Chinese officials and the World Health Organization say there is no evidence of sustained human-to-human transmission, despite occasional instances of apparent infection between family members.