Analyzes the current manufacturing informatization trend and the status of manufacturing execution system in enterprises′three level model, and studies the demand for the implementation of manufacturing execution system in automobile assembly enterprises based on the production mode of multiple varieties and small batch. Investigates MES overall structure design of automobile assembly enterprises from five aspects of system running environment, upper planning integration, intermediate process integration, bottom control integration and fundamental data information. Designs the MES function module for the order-driven multi-variety and small batch production mode of an electric automobile assembly Co. Ltd, and the research result is applied in the company′s production. The application shows that the proposed scheme gets good production efficiency.