Heilongjiang Province is the largest commodity grain production base in China, but the development of agricultural modernization still lags behind urbanization and industrialization. The problem of uneven agricultural development in various regions is still outstanding. Coordinating the level of agricultural development and production efficiency is the focus of agricultural development in Heilongjiang. Based on the analysis of the current situation of agricultural development in Heilongjiang Province, this paper measures the agricultural development level and production efficiency of 13 cities in Heilongjiang Province from 2006 to 2016 with the help of principal component analysis and DEA-Malmquist method, and analyzes the coordination between the two as well. The results show that the agricultural development level in most areas of Heilongjiang Province is relatively low in terms of agricultural production efficiency, and the uneven distribution of natural and social resources has gradually widened the gap between the coordination of agricultural development levels and production efficiency in various regions of the province. This article puts forward the suggestions for the development of modern agriculture in Heilongjiang Province as follows: develop facility agriculture on the basis of efficient production, and make full use of the characteristics and advantages of agricultural development in various regions according to the resource distribution characteristics of each region, and complement the development shortcomings.