The invention provides a flexible tool for drilling a profile part and a drilling method thereof, and belongs to the technical field of conventional processing techniques. The flexible tool comprisesa tool base, wherein a left-and-right adjusting device and an up-and-down adjusting device are arranged on the tool base, the structure of the left-and-right adjusting device is similar to that of theup-and-down adjusting device, the adjusting devices comprise lead screws, hand wheels, sliding blocks, sliding rails and fixed mechanisms, the back end of the tool base is connected with a general backing plate by virtue of a general bolt, a plurality of four-bar linkage crank clamp mounting holes are formed in the general backing plate, and a four-bar linkage crank clamp is fixedly connected tothe four-bar linkage crank clamp mounting holes by virtue of bolts. The flexible tool has the advantages of no need of marking by a bench worker, simple positioning and clamping mode, high efficiency,high part drilling quality and the like.