There was no immediate word of a settlement as the pilots' union remained firm in its demands for an additional backup pilot on flights lasting eight hours or more, a more transparent system of promotion, a year-end bonus and other concessions.
The official Central News Agency said a total of 47 flights will have been canceled by Sunday.
The strike came in the middle of the Lunar New Year travel rush. About 70 percent of the carrier's 1,300 pilots belong to the union, which has accused management of insincerity and mistreating its workforce to keep costs down.
CAL crews went on strike for 24 hours in 2016 for better conditions.
The airline has said it is willing to continue negotiations but that the union's demands in talks are different from those it makes in public.
Flights canceled included those bound for Hong Kong, Bangkok, Los Angeles, Manila and Tokyo. Most of those were departing from Taiwan's main international airport at Taoyuan, just south of the capital Taipei.
Founded in 1959, China Airlines is one of the island's two largest carriers with a fleet of 88 aircraft.