The coast guard dispatched patrol vessels after it received a report around 6 am Thursday (2200 GMT Wednesday) that a fishing boat carrying six people had sunk 1.07 nautical miles southwest of Kinmen Islands' Dongding islet.
Two crew members were rescued while two others "showed no signs of life", Taiwan's coast guard said in a statement.
The joint operation comes a month after the Taiwanese coast guard's pursuit of a Chinese fishing boat in the area left two men dead, further straining cross-strait relations.
Beijing claims democratic Taiwan as its own territory and has never renounced use of force to bring the self-ruled island under its control.
Administered by Taipei, Kinmen is located five kilometres (three miles) from the Chinese city of Xiamen.
Coast guard chief Chou Mei-wu told a parliamentary session Thursday that the fishing boat was "0.3 nautical miles within Taiwan's prohibited or restricted waters".
He added that both sides were striving to locate the missing within the "golden rescue time" of 72 hours.
Chou also recalled several previous joint rescue efforts by Chinese and Taiwanese authorities.
"In the past three years, we have had 17 cases like this where they (China) asked us for support, and we rescued 119 people," he said.
Taiwan's Premier Chen Chien-jen praised the rescue operation in parliament, saying previous efforts "have shown that China and Taiwan can work together in humanitarian aid".
By around 5 pm, Taiwan's coast guard told AFP "search and rescue is ongoing".
- Incident last month -
Last month, a Chinese boat carrying four people capsized near Kinmen while being pursued by Taiwan's coast guard.
Two of the crew died and two others were rescued and temporarily detained.
A survivor reportedly said the boat was "rammed", though Taiwan insisted the coast guard was following legitimate procedures after the vessel entered "prohibited waters".
Beijing accused Taiwan of "seeking to evade their responsibilities and hide the truth" about the incident, while a Taiwanese coast guard official has said the boat involved was zigzagging, "lost its balance and capsized" while trying to evade the patrol.
Since the February 14 incident, Taiwan's coast guard chief said an average of six to seven Chinese vessels have been seen in waters around Kinmen.
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