Periodic cruise has the potential to improve the fuel-saving efficiency of hypersonic cruise vehicles but is difficult to optimize. In this paper, hypersonic periodic cruise trajectory is analyzed theoretically and optimized by an improved Particle Swarm Optimization algorithm. Firstly, through theoretical analysis, it is determined that the optimal throttle curve can be parameterized as a switching function. Considering the optimization direction of algorithm, a new penalty function for the constraints of periodic cruise is proposed. Then, PSO algorithm is improved and applied in periodic cruise trajectory optimization. Numerical results demonstrate that optimized periodic cruise trajectory costs less fuel compared with steady-state cruise trajectory, and without computing gradient information, the proposed method is also robust. Finally, the fuel-saving mechanism of periodic cruise is explored by comparing with steady-state cruise, which reveals that periodic cruise trajectory has higher impulse and lift-drag ratio, but lower mechanical energy loss rate.