The defence ministry said the planes entered the area in two waves, during the day and during the evening.
It comes after 38 planes, including nuclear-capable bombers, entered the zone on Friday.
China sees democratic Taiwan as a breakaway province, but Taiwan sees itself as a sovereign state.
Taiwan has been complaining for more than a year about repeated missions by China’s air force near the island.
“China has been wantonly engaged in military aggression, damaging regional peace,” Taiwan Premier Su Tseng-chang told reporters on Saturday.
But it has previously said such flights were to protect its sovereignty and also targeted “collusion” between Taiwan and the US.
- EXPLAINER: What’s behind the China-Taiwan divide?
Taiwan’s defence ministry said 20 Chinese aircraft came during the day on Saturday with a further 19 entering the area during the evening.
An air defence identification zone is an area outside of a country’s territory and national airspace – but where foreign aircraft are still identified, monitored, and controlled in the interest of national security.
It is self-declared and technically remains international airspace.
Taiwan responded by scrambling its jets and deploying missile systems.
The ministry said the Chinese aircraft included four H-6 bombers, which can carry nuclear weapons, as well as an anti-submarine aircraft.
Beijing often launches such missions to express displeasure at comments made by Taiwan.
China and Taiwan: The basics
- Why do China and Taiwan have poor relations? China and Taiwan were divided during a civil war in the 1940s, but Beijing insists the island will be reclaimed at some point, by force if necessary
- How is Taiwan governed? The island has its own constitution, democratically elected leaders, and about 300,000 active troops in its armed forces
- Who recognises Taiwan? Only a few countries recognise Taiwan. Most recognise the Chinese government in Beijing instead. The US has no official ties with Taiwan but does have a law which requires it to provide the island with the means to defend itself.