After issuing an apology to impacted customers and providing refunds for passengers booked on Lunar New Year flights, a China Eastern spokesperson issued a statement on behalf of the airline about Taiwan's decision.
China opened the new air routes this month, including a northbound route up the Taiwan Strait.
Taiwan has expressed concern the new routes are too close to existing routes that link it to airports on two groups of Taiwan-controlled islands lying close to China, and are a threat to flight safety.
Taiwanese people hoping to get home for the holiday will have have to go via Hong Kong, Macau, or another country - or alternatively, says the BBC, "they could choose a Chinese airline or Taiwanese airline that had not been using the new routes, though tickets would be hard to come by".
The airlines said Taiwan's refusal to approve the new routes leaves them no choice but to cancel all 176 flights, a claim contested by Taiwanese officials.
The Civil Aeronautics Administration in Taiwan said that it was never consulted over the flight routes.
Taipei slammed the move as reckless and said it could threatened the island's security.
China considers Taiwan a wayward province, and relations have cooled since Ms Tsai Ing-wen of the independence-leaning Democratic Progressive Party took office as Taiwan's president in 2016.
The move has been viewed in Taiwan as a show of disrespect, one that could heighten the risk of a risky incident and potentially provoke a crisis in the increasingly tense cross-strait relationship.
At a press conference yesterday, Taiwanese Transport Minister Hochen Tan said the government did not force the airlines to cancel their flights.
Reports suggest about 50,000 passengers will be affected by the flight cancellations.
However, Taiwan claimed that no consultations were made over the planned routes that the airlines meant to fly their planes and levelled unilateral action accusations towards the Chinese government. Then direct flights were permitted, and they continue across the Taiwan Straits today.