Nan Juyi was a native of Weinan in Shaanxi who passed the metropolitan examinations in the Wanli reign. He became governor of Fujian in September 1623, a year after the Dutch had built their fort on Penghu. His predecessors had talked and waited for the Dutch to leave on their own.

He did not wait. Soon after he took office, the Ming side lured Dutch envoys at Xiamen into a trap, seized them and burned their ships, while troops and ships were gathered along the coast. In 1624 he sent Yu Zigao and others across in waves; by mid-August some ten thousand men and two hundred ships had massed on Penghu, penning the square fort at the tip of Fengguiwei.

The two sides agreed a truce on 22 August on clear terms: the Dutch would demolish the fort and leave Penghu; in return the Ming would not interfere if they went to Taiwan. In September the Dutch withdrew to Tayouan. In Ming reports this was the recovery of lost territory. Taiwan lay outside the realm, so letting them go there conceded nothing.

He later rose to Minister of Works. In 1644 Li Zicheng's army took Weinan; captured and refusing to submit, he starved himself to death. The island he had let the Dutch have was still in their hands that year.