Lee Ming-cheh -- an NGO worker arrested during a trip to the mainland last March -- was sentenced in November to five years in prison by a court in the central province of Hunan on charges of subverting state power.
Human rights and democracy activists have been targeted in Chinese President Xi Jinping's crackdown on dissent since he took power in 2012.
Taipei had called Lee's jailing "unacceptable" and a serious blow to cross-strait relations, while his wife Lee Ching-yu called his trial a "political show".
Lee Ching-yu had her mainland travel permit cancelled last April when she was trying to locate Lee, who was held incommunicado for months before his trial.
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Since then, Chinese authorities had only granted her single-entry visas to attend the trial and sentencing.
Taiwan authorities urged China Tuesday to issue the necessary permits for her.
"It is regrettable that China did not allow Ms Lee to board the plane to China today," the Mainland Affairs Council, which handles official contacts with Beijing, said in a statement.
Lee had admitted the charges during his trial in September, stating that he had written and distributed online articles that criticised China's ruling Communist Party and promoted democracy, among other topics.
He had shared "Taiwan's democratic experiences" with his Chinese friends online for many years and often mailed books to them, according to the Taiwan Association for Human Rights.
Lee Ching-yu -- who tattooed her husband's name on her arm before his trial -- has appealed for overseas support and testified at a US Congressional hearing last May.
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