In this paper, meta-synthesis system approach (MSA) is applied to a consulting project on exploring constructing comprehensive transportation system in China. Firstly, brief introduction about the concept of comprehensive transportation is given to indicate that comprehensive transportation is an open complex giant system, which thus MSA is applied to exploring its constructing in China. A group argumentation environment (GAE) is applied to facilitate group divergent thinking process about what the concerned topics are in the project and acquire qualitative hypotheses for meta-synthetic system modeling. A multi-agent system model is constructed to analyze competitive relations of passenger transport between railway and highway as a demonstration of modeling by rule, one of 6 strategies of meta-synthetic system modeling. An evaluation support system is developed to integrate a variety of indicators and their related measure methods by a framework of input-output-outcome of comprehensive transportation to facilitate consultants to monitor current state of operation and management of transport system and generate alternatives of a set of indicators to evaluate efficiency or effectiveness of the whole system or its elements on demand. Firstly, brief introduction about the concept of comprehensive transportation is given to indicate that comprehensive transportation is an open complex giant system , which thus MSA is applied to exploring its constructing in china. A group argumentation environment (GAE) is applied to to explore its constructing in. a multipoint -agent system model is constructed to analyze competitive relations of passenger transport between railway and highway as a demonstration of modeling by rule, one of 6 strategies of meta-synthetic system modeling. An evaluation support system is developed to integrate a variety of indicators and their related measure methods by a framework of input-output-outcome of comprehensive transportation to facilitate consultants to monitor current state of operation and management of transport system and generate alternatives of a set of indicators to evaluate efficiency or effectiveness of the whole system or its elements on demand.