Land use zoning is the basis and key elements of the overall land use planning. It is important to determine the future land use direction, formulate the land use structure and spatial layout adjustment strategy, and realize the regional land differentiation management and sustainable utilization. As the most important commodity grain base in China, Northeast China has a significance to the national food security. However, the economic development level of different provinces in Northeast China is quite different. The development of regional economy is unbalanced.The index system of characterizing the three-dimensional state of land use in the main grain producing areas was constructed, and the two-dimensional graph theory clustering method and GIS spatial analysis method were used to study the land use zoning of 184 county-level administrative units in northeast region, and differentiated land use regulation measures were put forward. The results showed that the three-dimensional evaluation index system of land use can clearly reflect the natural background condition, development status and future development potential of land use;the results of land use zoning in Northeast China obtained by two-dimensional graph clustering and GIS qualitative analysis had good spatial continuity as well as zoning integrity, which improved the feasibility and scientificalness of land use zoning. The northeast region was divided into twelve zones consisted of three city comprehensive development zones, two agricultural and animal husbandry land use zones, one agricultural and forestry land use zone, one agricultural, forestry and animal husbandry land use zone, five forestry and agricultural ecological zones. The research had certain reference significance for the management of land use in the main grain producing areas.