In order to scientifically evaluate the harmony degree of water resources-economic society-ecological environment coupling system in the Tarim River Basin and make clear the main factors that affect its harmonious development, a harmony evaluation index system of water resources-economic society-ecological environment coupling system is constructed, considering water resources endowment, regional development level and ecological environment condition. The harmony degree of each subsystem and coupling system in five regions of Tarim River Basin from 2007 to 2016 was quantitatively calculated by using combination weight SMI-P method. The results show that, in time dimension, the harmony degree of coupling system has been improved, but there are differences in speed and range, and none of them has reached the basic harmonious state, most of them are in the non-harmonious state; in spatial dimension, Bazhou coupling system is the best, and it is the only region to reach a relatively harmony degree, followed by Kezhou and Aksu Prefecture, while Hotan and Kashgar Prefecture are obviously behind the other three regions; the contribution of each subsystem to the harmony degree of the coupling system is ecological environment, economic society and water resources from big to small, and the contribution rate has significant space-time difference; there is still much room to improve the harmonious development level of each state. We should break through their weak links while coordinating the balanced development of multi-system.