Function area layout of underground distribution center is an important part of urban underground distribution center planning so that it would indirectly affect the building and development of underground distribution center and even the whole urban underground logistics system. Based on Automod simulation platform, the function area layout planning method was built in order to avoid underground operation invalidation because of the illogical function area layout. First by analyzing relative operation of underground distribution center, multi-objective 0-1 mixed integer programming model of function area layout was built based on two indexes of relativity and transit cost among function areas. Then the heuristic algorithm or exact algorithm was used to solve the mathematical model mathematical model and find out the layout scheme after quantifying the indicators. Finally the final layout was gained by simulation and optimization of Automod simulation platform. There was an example for proving the feasibility of the method. The results showed that the method was available to analyze the function area layout impact and it was very important for decision-making of building the underground distribution center.