In order to promote the construction of China's modernized agriculture, from the perspective of ecology,this paper adopts the SBM-DEA super-efficiency model based on undesired output under the meta-frontier theory framework to measure the government's agricultural investment efficiency of 31 provinces and cities in China from 2007 to 2016, and has carried out the spatial autocorrelation analysis. The results show that the eastern part of China has the highest efficiency, and the technical level of Shanxi in the central and western parts of Chongqing and Inner Mongolia has a lot of room for improvement. For each region, Hainan is the highest and Shanxi is the lowest. The high efficiency range is gradually spreading from the east to the middle, more and more central regions have improved efficiency. The low efficiency range is gradually shifting to the northwest. Therefore, China must change its agricultural production model, develop modernized agriculture according to local conditions, strengthen exchanges and cooperation between regions, and strengthen ecological control.