Lee Ching-yu was planning to fly to Beijing Monday afternoon in her bid to "rescue" husband Lee Ming-cheh, who is under investigation in China for suspected activities "endangering national security".
But she was told by the airline that she could not board the plane because her travel permit to the mainland has been revoked.
"I am surprised, shocked and saddened. Does the Chinese government really need to exercise so much power to stop a weak woman like me from going?" she told reporters at the airport near Taipei, her voice cracking with emotion.
Beijing deeply mistrusts her independence-leaning Democratic Progressive Party, and has severed official communications with Taipei since she took office.
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NGO worker Lee, 42, was last heard from on March 19 before he entered the southeastern Chinese city of Zhuhai from the semi-autonomous city of Macau.
"The government strongly protests that China bars Ms Lee from visiting by revoking her valid travel documents," said Chiu Chui-cheng, vice chairman of the Mainland Affairs Council, Taiwan's top policymaking body on China.
Taiwanese rights groups said Lee was first person detained since a Chinese law governing the activities of overseas NGOs went into effect this year.
Lee, also known as Li Ming-che, had been sharing "Taiwan's democratic experiences" with online Chinese friends and sent them books, according to a petition for his release led by the Taiwan Association for Human Rights.
Lee, who works for a community college in Taipei, also told his friends to donate to the families of human rights lawyers detained by China, the petition said.
Taiwan has been self-ruled since 1949 following a civil war on the mainland. But Beijing still claims it as part of its territory awaiting reunification, by force if necessary.