In order to meet the requirement of Flexible Manufacturing System, tool management, including tool preparation and tool setting, has to be planned systematically at the beginning of manufacturing engineering planning and flexible manufacturing line planning based on lean manufacturing principles. The objective of this article is to study the tool management factors that lean and flexible manufacturing system required, based on the planning of tool management in a new engine factory. This article introduces the main contents of tool management systems, analyzes the process of tool management, and summarizes the steps of tool planning process. In details, this article includes planning on tool management procedures, plant floor layout and information system. In addition, the article puts forwards a formula for calculation of tool presetting time, so that the demand of tool equipment quantity and personnel in a tool presetting room can be decided. This article can be used as reference or assistance to engineers as they develop tool management systems for engine manufacturing systems.