TRISO-Model (tridimensional integrated software development model) is a 3-D integrated software engineering methodology proposed to deal with the problems caused by the increasing complexity and dynamic in current software development. In TRISO-model, to maintain the semantic consistency among multiple models and reuse the common model operations, there is the need for semantic-consistent model management. This paper proposes an MDA-based model management method: MDA-MMMethod (MDA based model management method). Based on the common semantic definition—MOF (meta object facility), the implementations of MDA (model driven architecture) standards can be reused in the development of model applications in TRISO-model. The corresponding supporting system, MDA-MMSystem (MDA based model management system), is developed. Based on the system, this method is implemented in SoftPM project. Compared with the traditional solutions, the development efficiency is greatly improved and the cost is reduced. Finally, one example of the model applications and model merging is provided.