Wire electrical discharge machining (WEDM) is widely considered as a thermal removing workpiece material machining method, and it has many excellent abilities, such as ignored of workpiece thickness, good workpiece surface quality and no cutting stress. However, the thermal removing process will form heat stress in workpiece. The thinwalled part (with thickness, h<2 mm) will form thermal deformation, and this fact limits the application of WEDM in precise thinwalled part field. Analysis of the thermal balance of WEDM machining thinwalled part was conducted to reveal the formation mechanism of thinwalled part thermal deformation. Additionally, a set of Taguchi experiment and variance analysis method were implemented to obtain the influence trends of process parameters on the thermal deformation, and the root reason of these influence trends were clarified. Finally, according to the result of variance analysis, the process parameters for the minimal thermal deformation could be acquired. Verified experiment result shows that the minimal thermal deformation can be as low as 370 μm with the optimal parameters.