The lean Manufacturing Execution System (MES) and the characteristics of ship pipe fitting processing are summarized, and the functional structure of lean MES is expounded in detail. The thinking method of lean production in the lean MES is penetrated throughout the system development and application, and is successfully applied in the whole-flow production of ship pipe fitting processing to reform the traditional flow, realize the digitization of production flow by the informatization means, and perform an optimal configuration of enterprise production resource, thus to prompt each production link in the enterprise more lean and efficient. The successful application of lean MES in ship pipe fitting processing workshop is of certain reference and guiding significance for the transformation and upgrading of other domestic ship enterprises.