Considering that the Store Management System (SMS) is becoming more and more complicated, we used the method of Model-Based Systems Engineering (MBSE) in the development of SMS for the first time. With the Harmony method, and by use of such tools as DOORS and Rhapsody, we made requirement analysis, system function analysis, architecture analysis and design of a system, obtained a series of use case models and interfaces, and implemented the validation of requirements and analysis of the system. Compared with the traditional design method taking documents as the center, the MBSE based method verifies and traces the requirements more adequately, and is able to avoid iterative designs caused by departure from the requirements, and thus the development efficiency can be improved.