Based on the interaction mechanism of harmonious development among new rural economy, transportation and rural ecological environment, the paper established coupling coordinative degree index system and made an empirical analysis on the coupling harmonious development of new rural economy - transportation - rural ecological environment of Yunnan province during the years between 2007 and 2016 by using coupling harmonious degree model. The result found that the comprehensive development level of these three systems was in a steady rise trend, while the rural ecological environment comprehensive evaluation index was volatile and experienced the undulation of rising first, and then falling and rising again. In recent years, the degree of coupling coordination shows a steady upward trend. As a whole, the three systems realized the change of improvement from slight imbalance recession to primary coupling coordination, but the coupling coordination relation of new rural economy - transportation - rural ecological environment was in a state of rivalry, and coupling coordination level was still relatively low. The development of rural ecological environment system lagged behind, becoming the obstacle factor that restricted the improvement of the level of coupling coordination among the three systems. According to the research results, the article proposed the corresponding conclusion and suggestion.