Abstract: Apple industry has become a major industry of rural economy in most of the north region in China, which plays an important role on the adjustment of agricultural structure, the increase of farmer's income and the export. But overall, the development of apple industry still has belonged to the traditional production style depending on fertilizer and pesticide; on one side it has brought high economic benefits for farmers, and on the other side it has been the main reason to agricultural non-point source pollution. There is no doubt that this production style has exacerbated the contradiction between the development of apple industry and the ecological environment in China. Therefore, in order to achieve the sustainable development of apple industry, the transformation of the development mode of apple industry, the improvement of resource use efficiency and the effective control of non-point source pollution in apple production should be taken into account urgently. And to achieve these goals are closely dependent on the contribution of apple total factor productivity to industry development, the reasonable estimation of apple total factor productivity, and thus the guide of the correct policy. Using the unit investigation and evaluation model, this paper calculates the non-point source pollution from apple industry, which is taken as non-ideal output and integrated into the model of total factor productivity, then analyzes the total factor productivity of apple industry under the constraint of environment of 21 provinces in China from 1994 to 2013 by applying the Malmquist-Luenberger productivity index, and finally tests the spatial autocorrelation of total factor productivity of apple industry by using Moran's index. The results show as follows: 1) Apple total factor productivity index under the constraint of environment is lower than that without this constraint, implying that environment pollution has obvious negative effects on apple productivity in China, and the development of apple industry presents extensive growth at the expense of polluting environment; at the same time the Malmquist index overestimates the contribution of technical efficiency and technical progress rate to apple total factor productivity. 2) Apple total factor productivities in different regions have obvious difference. Specifically, the growth rate of "good" output in Shaanxi, Ningxia, Yunnan and Guizhou is lower than the decreasing rate of "bad" output, and conversely the growth rate of "good" output in Shandong, Liaoning, Beijing and Tianjin is higher than the decreasing rate of "bad" output, which means the development of apple industry in the central and western China does not coordinate with environment, and conversely the development of apple industry in eastern region is in harmony with the environment. 3) Apple total factor productivity under the constraint of environment shows the significantly positive spatial correlation in both global and local level, but spatial association types of total factor productivity in different provinces during the sample period change obviously. Apple total factor productivity in specific provinces presents the spatial distribution characteristics of high-high aggregation, which takes Shaanxi, Gansu and Shanxi as the center. These results suggest that the government should strengthen the research and promote the environmentally-friendly technology related to apple production like soil-testing formula technology; the governments of different provinces should formulate the environmental management policy related to apple industry based on local conditions, and promote the development of apple industry in harmony with the environment. For instance, the western regions should draw lessons from the eastern coastal areas about apple's advanced production technology, improve the utilization rate of fertilizer, and reduce the gap between regions; different apple production provinces should strengthen the cooperation, pay more attention to and use the spatial spillover effect of apple total factor productivity, and then enhance driving force and radial force of apple total factor productivity of high-high aggregation areas.