In order to solve the problems in the implementation of MES system, the implementation problem of MES system in the assembly industry were analyzed. The background and management mode of the production line are introduced, and the main problems in the production management, such as data transmission between systems, labor dispatch, product process to be processed and material code scanning, are respectively described. The main problems in the logistics management, equipment management and system operation and maintenance are analyzed, and the ideas to solve the problems are put forward. This idea has certain practical value.