Jilin is an important grain producing area and heavy industry base in China. With the economic development and improvement of people's livelihood, water resource issues have been becoming increasingly prominent, Jilin Province comprehensive utilization of water resources is not efficient. The traditional method of water consumption per 10000 Yuan of output value cannot objectively reflect the water-use efficiency of different local industrial structures. Therefore, this paper builds the data envelopment analysis model based on the input-output relationship. In order to meet the requirements of data envelopment analysis model for data analysis, this paper introduces the principal component analysis method, and reduces the 16 water resources input indicators and 14 water resources output indicators of Jilin Province from 2004 to 2017 to 3 input principal components and 2 output principal components. The multi-model data envelopment analysis method is used to analyze the water-use efficiency of Jilin Province, and the results show that with the rapid economic growth, the water resources efficiency in 2010-2013 was relatively poor, there was a waste of water resources, and the management technology was backward, but with the deepening of the industrial transformation and upgrading, farming modernization and revitalizing the strategy of the old industrial base in Northeast China, the water-use efficiency and the water resources carrying capacity of Jilin Province has been improved.