Abstract: Taizhou-Wenzhou Regional Rail Transit Connecting Line (Wen-Tai Line for short) is 54.95 kilometers long, connecting Wenzhou regional rail transit Line S2 and Taizhou regional rail transit Line S1. The organization scheme of the 3 lines will play an important role for the overall layout of rail transit in this metropolitan area. In this paper, the line operation design analysis method is used to study the all-through, partly-through and independent operation organizations. The research result shows that the partly-through operation scheme is a balancing act for passenger flows on both the local Wen-Tai Line and the cross-line by adopting the cross-line interchange and short-turn routing modes, but the terminals on both ends of the Wen-Tai Line should be reformed. The partly-through operation leaves some leeway for both engineering design and diversified investment, and therefore is a reasonable and achievable scheme under consideration.