With the further development of urbanization, the rail transit system with the integration of multiple modes is exerting more and more important influence on regional development. “Four networks integration” will boost the sound and rapid development of regional economy. Wenzhou is an important city in Yangtze River Delta. In recent years, the government put forward to build national central hub city . In this context, the promotion of "four networks integration" is particularly significant. Focus on the comprehensive cohesion of region express rail and railway, this paper analyzed the status of Wenzhou rail transit system. Passenger flow characteristics, the distribution of lines and networks, train operation plan and so on are researched at the beginning of the paper.In order to improve the connection of the first and last train of different standard rail transit systems, several optimization schemes for the first and last trains were put forward. In view of these problems, some improvement measures are put forward. The necessity and feasibility of the interconnection between the national railway and the region express rail is analyzed in this paper. The conclusion in this paper has reference value for the connection optimization of Wenzhou multi-system rail transit system. The evaluation index system is also valuable in the practice of similar systems.