The incident happened Tuesday near Qimei island, which is part of the Taipei-administered Penghu archipelago in the sensitive strait separating Taiwan and China.
Images released by the coast guard showed its ship pursuing the fishing boat and then its personnel boarding the vessel where they found about one tonne of fish.
In a statement, the coast guard said its vessel had broadcast warnings and deployed water cannon during a high seas pursuit of the fishing vessel.
The fishing boat was towed to Qimei port on Wednesday and an investigation was underway.
"We urge the public to report any sightings of unauthorised Chinese fishing vessels... as part of a continued effort to safeguard national security and development of marine resources," Penghu Coast Guard said.
China claims self-ruled Taiwan as part of its territory and relations between the two have deteriorated in recent years.
Taiwanese and Chinese coast guard boats regularly patrol the Taiwan Strait.
A series of incidents involving boats from both sides have fuelled tensions across the narrow waterway.
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