In order to achieve more precise control of the urban railway transportation Auto-matic Train Operation(A TO) system， by analyzing traditional PID control theory， this pa-per explores the detailed process of positional PID control algorithm and realizes the process using modern computer science.This paper also studies howto combine positional PID con-trol algorithm and state equation and the possibility and methods to apply the improved ver-sion to the above-mentioned A TO system：by changing three parameters in the equation of the algorithm， the most suitable coefficient will be obtained for the A TO system to decide the precise timing for traction and braking.The results show that application of positional PID control algorithm can control the train with greater accuracy achieve energy conserva-tion by decreasing the time of traction and braking and improve the comfort and stability by stable speed increase.