Abstract: This paper analyzes the present development of Model-Based Systems Engineering（MBSE）, the problems and challenges of system engineering for deep space exploration and MBSE, and proposes that the digital engineering ecology is the development direction of the new generation of MBSE for deep space exploration mission. It summarizes the Model-Based System Engineering method framework for deep space exploration mission collaboration. The “four closed loop iteration” process method is proposed to support deep space exploration task collaboration, and the system model system and tool chain platform supporting deep space exploration MBSE are analyzed comprehensively. Based on the characteristics of deep space exploration mission, this paper discusses the collaborative design and continuous verification technology of cross specialty, cross level, cross phase and cross region, as well as the model-based safety and reliability quality management and technical state control technology. Finally, the content points and key trends of the new generation of model-based digital system engineering for deep space exploration are summarized and expected.