Piezoelectric actuator (PEA) has been widely used in micro-systems, due to the advantages of nano-scale precision, rapid response speed, high stiffness, etc. Nevertheless, the intrinsic nonlinearities of PEA, particularly hysteresis, severely deteriorate its positioning and tracking control accuracy. In most existing control algorithms of PEA, the approximate inverse model of hysteresis is developed to compensate for motion error, which requires high modeling accuracy. To avoid the influence of complex modeling procedures and modeling errors on tracking precision, a trajectory compensation-based adaptive control method has been proposed in this paper. Firstly, a simple linear controller is used to establish the closed-loop feedback system and to guarantee the basic tracking performance of the PEA system. And then, the trajectory compensation is designed according to the frequency analysis of the closed-loop control system. Finally, nonlinear adaptive compensation is used to eliminate the residual errors of the above linear frequency domain model. Different from conventional controllers, the proposed method can achieve excellent tracking control performance without any hysteresis model of PEA. The stability and convergence of the proposed method have been theoretically proved. In addition to theoretical guarantees, the proposed method is validated experimentally and demonstrated to achieve the root-mean-square and maximum value of tracking errors to less than 8 nm and 25 nm, respectively, which has a clear accuracy advantage over other methods.