Based on the interaction mechanism of harmonious development of new rural economy, transportation and rural ecological environment, the paper introduces coupling and coordination evaluation system and analyzes the coupling harmonious development of new rural economy, transportation and rural ecological environment in Yunnan province from 2007 to 2016 by using coupling harmonious degree model. The results show that the comprehensive development level of these three systems is in the trend of increasing, while the rural ecological environment comprehensive evaluation index fluctuates greatly, and presents 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 have realized the change of improvement from slight imbalance recession to primary coupling coordination. However, the coupling coordination relationship of new rural economy-transportation-rural ecological environment is in a state of rivalry, and coupling coordination level is still relatively low. The development of rural ecological environment system lags behind, becoming the obstacle to the improvement of the level of coupling coordination among the three systems. Finally, this paper proposes corresponding suggestions.