German flagship carrier Lufthansa had already cancelled 912 flights for Thursday, grounding 115,000 more passengers.
The first day of the strike on Wednesday saw nearly 900 flights cancelled and around 100,000 passengers were affected after pilots staged a walkout in a row over pay and working conditions.
In total, the three-day strike will impact more than 315,000 passengers, Lufthansa said.
Late Wednesday, pilots' union Cockpit called for the strike – its 14th since April 2014 – to continue through Friday, urging short-haul flight pilots to stay off work.
Meanwhile a separate walkout by cabin crew at Lufthansa's low-cost airline Eurowings led to the cancellation of more than 60 flights at airports in Hamburg and Düsseldorf on Tuesday.
The Lufthansa pilots going on strike are demanding a pay rise of an average of 3.66 percent per year, retroactive for the past five years.
Their union says pilots have endured a wage freeze over that time and suffered a “significant loss of purchasing power” due to inflation, while Lufthansa has made billions in profits.
It had offered a 2.5 percent wage hike.
Lufthansa urged the Cockpit union to work towards a resolution rather than escalate the problem.
“Cockpit's demand for a pay rise… goes far above what other groups of employees have received. It is incomprehensible why the union is seeking the highest salary increase for the best paid group of employees,” said Bettina Volkens, Lufthansa's human resources chief.
Lufthansa has been battling a series of walkouts by both cabin crew and pilots over the last two years, as it battled to bring down costs to survive competition from low-cost rivals such as EasyJet and Ryanair.
In July, it brought an end to the long-running industrial dispute with cabin crew through a deal on pay and working conditions, including a no-strike agreement and job guarantees until 2021.
Lufthansa group's other airlines – Germanwings, Swiss, Austrian Airlines, Air Dolomiti and Brussels Airlines – are not affected by this week's strike.