Abstract: Based on energy analysis theory, GIS spatial analysis technology and the socio-economic statistic data available of the 77 counties of Heilongjiang Province, comprehensive assessment was done, from the angle of spatio-temporal dynamics, of structures and overall development levels of the agro-eco-economic systems of Heilongjiang and its 77 counties. Results show that both the input and output in energy value of the agro-eco-economic system of the province displayed obvious growing trends, especially that of the energy output of the forestry during 1996-2012. Moreover, the agro-eco-environment of the studied region was exposed to an increasing pressure. For example, the environmental loading factor increased from 6.61 to 10.21, the net energy output decreased from 5.37 to 4.79, and the energy sustainable development index declined from 7.47 to 5.43, all demonstrating that the system was gradually weakening in sustainable development performance. Spatially, the economic development level in the southern part of the province was significantly higher than that in the northern part. However, a reverse trend was found in agricultural ecological environment and sustainable development capacity. In order to bring the agricultural eco-economic system onto the track of sustainable and stable development, it is essential in future to further readjust the agricultural structure, optimize resources allocation, improve resources utilization efficiency, and reduce the environmental load.