Time of arrival (TOA) measurement is a promising method for target positioning based on a set of nodes with known positions, with high accuracy and low computational complexity. However, most positioning methods based on TOA (such as least squares estimation, maximum-likelihood, and Chan, etc.) cannot provide desirable accuracy while maintaining high computational efficiency in the case of a non-line of sight (NLOS) path between base stations and user terminals. Therefore, in this paper, we proposed a creative 3-D positioning system based on particle swarm optimization (PSO) and an improved Chan algorithm to greatly improve the positioning accuracy while decreasing the computation time. In the system, PSO is used to estimate the initial location of the target, which can effectively eliminate the NLOS error. Based on the initial location, the improved Chan algorithm performs iterative computations quickly to obtain the final exact location of the target. In addition, the proposed methods will have computational benefits in dealing with the large-scale base station positioning problems while has highly positioning accuracy and lower computational complexity. The experimental results demonstrated that our algorithm has the best time efficiency and good practicability among stat-of-the-art algorithms.