To solve the problem that the optimal average station spacing guidance does not play a significant role in the actual layout of the stations, the model and algorithm optimization of the site distribution of urban rail transit station is proposed. Firstly the city radius is defined, and the city was divided into three types, and rail transit lines was divided into two types, the rail transportation average station distance model was established and solved based on the city scale, respectively. The line was divided into obstacles, connected region and the feasible region, according to the area line through is constructly or not. And then the stations was divided into three grades according to the station passenger flow and the functional layout of the area line through. Station location model was established and optimized. Finally, the optimal average station spacing and each site layout position can be solved by proposed model, in the case of Changchun light rail line 4. Light rail line 4 peak hour capacity was increased by 6%, site distribution of the model compared with the existing site.