Concerning the coverage overlapping areas and blind spots caused by random deployment of nodes in three-dimensional directional heterogeneous network, a Particle Swarm Optimization (PSO) based coverage optimization algorithm for three-dimensional directional heterogeneous network, namely PSOTDH, was proposed. Through involving the concepts of three-dimensional overlapping centroid, three-dimensional effective centroid and three-dimensional boundary centroid, three-dimensional overlapping area, and three-dimensional boundary nodes were optimized in a new three-dimensional directed perception model by using PSO. The sensing directions of the nodes were changed by PSOTDH, which made the distribution of three-dimensional overlapping centroids, three-dimensional effective centroids and three-dimensional boundary centroids more uniform, and achieved the purpose of improving coverage. Simulation results show that the proposed algorithm can improve coverage rate by about 27.82% after 25 iterations, which means the proposed algorithm can improve the coverage rate quickly and effectively.