This paper presents a rapid initial three-dimensional low-thrust trajectory design method based on the layered strategy of shaping theory and intelligent optimization algorithm. The outer layer uses particle swarm optimization algorithm to optimize the flight time within the feasible range and the inner layer solver approximates the rendezvous trajectory through finite Fourier series, greatly improving computational efficiency by converting it into a finite parameter optimization problem. During the iteration process, the initial flight time is estimated by using the required velocity increment for non-coplanar circular orbit maneuvers, and the feasible range of flight trajectory revolutions is qualitatively analyzed based on boundary conditions and thrust constrain, efficiently initiating this method automatically. The results show that this approach can rapidly generate three-dimensional rendezvous trajectory in different scenarios with high accuracy. This is quite favorable for the rapid feasibility assessment of a great many of alternative trajectories in the preliminary phases of mission design.