The invention provides an automatic assembly type photodynamic drill based on multi-core fiber. The automatic assembly type photodynamic drill comprises front optical tweezers and a micro rotor formed by processed multi-core fiber. In solution the optical tweezers automatically captures the micro rotor to form a photodynamic drill. The micro rotor structure comprises a ball, a rotating shaft, a windmill like rotor structure composed of a plurality of wings and a cone tip, wherein the ball is at the top of the rotating shaft, the windmill like rotor structure composed of a plurality of wings is at the middle of the rotating shaft, and the cone tip is at the bottom of the rotating shaft. According to the invention, the micro rotor ball can automatically form a photodynamic drill once captured. The photodynamic drill has the advantages of convenient operation, simple structure, and easy control. The dimension of the photodynamic drill is micron-sized, and the rotating speed is easy to control from outside. The photodynamic drill can be applied to microbe punching such as cell wall punching. Accordingly, the automatic assembly type photodynamic drill based on multi-core fiber providesa strong tool for micro life science and biomedical researches.