The invention provides a UUV trajectory tracking control method for preventing the differential explosion based on the differential output characteristics of a biological instructive model. The method comprises the following steps of 1, conducting the initialization; 2, obtaining position and attitude error variables based on an under-actuated UUV mathematical model; 3, calculating a virtual control law, and replacing a virtual expectancy control law with the output value of the biological instructive model; 4, constructing a Lyapunov function, and transferring the ballast of a position error to the ballast of a speed error, avoiding the differential explosion phenomenon through the real-time derivation of replacing a virtual control variable with the output of the biological instructive model, and realizing the ballast of the speed error; and 5, designing a trajectory tracking controller. According to the technical scheme of the invention, the differential explosion phenomenon caused by the repeated derivation of the traditional back-stepping method can be avoided, and the complexity of the controller is simplified. Meanwhile, in combination with the controller of the biological instructive model, the time constraint requirements of the thrust constraints and the under-actuated UUV trajectory tracking of a propeller on position, speed and attitude can be met.