Guzaili Nu'er said she received the arrest warrant today and learned that her husband, Ilham Tohti, is being held in a detention centre in the far-western region of Xinjiang, a centre of low-intensity but frequent insurgency.
The arrest of Ilham Tohti came as Beijing is stepping up security in the region.
Xinjiang officials were not immediately available for comment after working hours. A statement by local authorities in January accused Ilham Tohti of spreading separatist ideas, inciting ethnic hatred and engaging in separatist activities.
He is a critic of the ruling Communist Party's restrictive policies in Xinjiang, but has not joined calls for Xinjiang's independence.
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"My husband is a college professor, a Uighur scholar. The description by the government does not fit him," Guzaili Nu'er said. "How could the university have allowed him to do what (the authorities) have alleged?"
His lawyer, Li Fangping, said that he had travelled to Urumqi, the capital of Xinjiang, but had not been allowed to visit Ilham Tohti.
The charge is punishable by 10 years to life in prison, or the death penalty if authorities find the crime to be particularly objectionable.