The defence ministry said it tracked 49 warplanes and 19 navy vessels, as well as Chinese coast guard vessels.
Thirty-five of the planes flew across the median of the Taiwan Strait, the de facto boundary between the sides, over a 24-hour period to today.
"Facing external challenges and threats, we will continue to maintain the values of freedom and democracy," Taiwan's new President Lai Ching-te told sailors and top security officials as he visited a marine base in Taoyuan, just south of the capital, Taipei.
In his inauguration speech on Monday, Lai had called on Beijing to stop its military intimidation and said Taiwan was "a sovereign independent nation in which sovereignty lies in the hands of the people".
China accused of 'piracy' after boats rammed, guns stolen in disputed sea
China's military said its two-day exercises around Taiwan were punishment for separatist forces seeking independence.
It sends navy ships and warplanes into the Taiwan Strait and other areas around the island almost daily to wear down Taiwan's defences and seek to intimidate its people, who firmly back their de facto independence.
"As soon as the leader of Taiwan took office, he challenged the one-China principle and blatantly sold the 'two-state theory'," China's Taiwan Affairs Office spokesman Chen Binhua said in a statement on Thursday night.
The one-China principle asserts that there is only one China and that Taiwan is part of China under Communist Party rule.
Beijing views Taiwan as a renegade province and has been upping its threats to annex it by force if necessary.