As the “first service station” for ships in the whole port logistics system, the tugboat operation system is one of the most important systems in port logistics. This paper formulated the tugboat scheduling problem as a multiprocessor task scheduling problem (MTSP) after analyzing the characteristics of tugboat operation. The model considers factors of multianchorage bases, different operation modes, and three stages of operations (berthing/shifting‐berth/unberthing). The objective is to minimize the total operation times for all tugboats in a port. A hybrid simulated annealing‐based ant colony algorithm is proposed to solve the addressed problem. By the numerical experiments without the shifting‐berth operation, the effectiveness was verified, and the fact that more effective sailing may be possible if tugboats return to the anchorage base timely was pointed out; by the experiments with the shifting‐berth operation, one can see that the objective is most sensitive to the proportion of the shifting‐berth operation, influenced slightly by the tugboat deployment scheme, and not sensitive to the handling operation times.