"Out of the 430 flights scheduled on Thursday, 158 have been cancelled," a Germanwings spokesman told AFP.
And on Friday, 180 out of a total 474 flights would be grounded, he added.
Germanwings operates many of Lufthansa's domestic and some of its European services.
Pilots' union Vereinigung Cockpit staged a long series of walkouts last year over management plans to change the pilots' transitional pension arrangements.
Currently, pilots can retire at 55 and receive up to 60 percent of their pay until they reach the statutory retirement age of 65.
Lufthansa wants to scrap the arrangement.
Germanwings added that "more than 60 percent" of the 900 flights scheduled for Thursday and Friday would operate. Aircraft and pilots would be borrowed from other airlines including Lufthansa, Swiss and Austrian Airlines.
On some of the affected flights, passengers would be given tickets to travel by rail instead, the spokesman said.
Passengers can check whether their flight is going ahead on the Germanwings website.