In order to design a management information system to satisfy the demand for the seedling production in China, this article takes the grafted seedling production as an example to analyze the management process (inventory management, production planning, quality control, and so on) in a seedling enterprise. The ERP (enterprise resource planning) management method is applied to design the system. In order to achieve the information management and provide decision support for the overall management, expert knowledge in the form of database and models is used as a key solution to uncertainties that affect the agricultural production. The browser/server architecture (B/S) is adopted to design the system for a flexible deployment and a low total cost of ownership (TCO). The result shows that the system is steady and effective to manage information during the seedling production, and could be a tool for data processing and information management. The research and analysis of the seeding production management system based on ERP provide theoretical basis for the standard business process of agricultural enterprises.