Rapid transit is important for the green development of China’s tourism industry because it profoundly affects the optimal structural layout and rational allocation of elements that impact regional tourism. Based on provincial panel data from 2009 to 2020, the entropy weight method, tourism carbon emission measurement model, Super efficiency slacks-based measure model and threshold regression model were used to determine the impact of the rapid transit system on tourism eco-efficiency in China. The findings showed that rapid transit system has increased steadily, while tourism eco-efficiency has fluctuated significantly, and the relative development characteristics of rapid transit system and tourism eco-efficiency gradually changed from “lagging rapid transit system” to “lagging tourism eco-efficiency.” In addition, the rapid transit system and the highway and civil aviation have a nonlinear relationship with tourism eco-efficiency, while the high-speed railway has not passed the threshold effect test, and at the regional level, the impacts of rapid transit system have heterogeneous characteristics. As the deepening construction of rapid transit system, its threshold effect on tourism eco-efficiency will change from positive “V” to positive “U” type, promoting the more efficient development of environmentally friendly tourism.