The move follows a proclamation by President Donald Trump in May aimed at Chinese nationals suspected of having ties to the military. He said some had stolen data and intellectual property.
The state department gave no details. China has not commented.
Nearly 370,000 students from China enrolled at US universities in 2018-19.
A state department spokeswoman described those declined a visa as "high-risk graduate students and research scholars."
She said they were a "small subset" of the total number of Chinese students.
"We continue to welcome legitimate students and scholars from China who do not further the Chinese Communist Party's goals of military dominance," the spokeswoman said.