Cultivated land use layout adjustment (CLULA) based on crop planting suitability is the refinement and deepening of land use transformation, which is of great significance for optimizing the allocation of cultivated land resources and ensuring food security. At present, people rarely consider the land suitability of crops when using cultivated land, resulting in an imbalance between crop distribution and resource conditions such as water, heat, and soil, and adversely affects the ecological security and utilization efficiency of cultivated land. To alleviate China’s grain planting structural imbalance and efficiency loss, this paper based on the planting suitability of main food crops (rice, soybean, and maize) to adjust and optimize the cultivated land use layout (CLUL) in the typical counties of the main grain production area in Northeast China, using the agent-based model for optimal land allocation (AgentLA) and GIS technology. Findings from the study show that: (1) The planting suitability of rice, soybean, and maize in the region is obviously different. Among them, the suitability level of soybean and maize is high, and that of rice is low. The current CLUL of the food crops needs to be further optimized and adjusted. (2) By optimizing the layout of rice, soybean, and maize, the planting suitability level of the food crops and the concentration level of the CLUL spatial pattern have been improved. (3) The plan for CLULA is formulated: The study area is divided into rice stable production area, maize-soybean rotation area, maize dominant area, and soybean dominant area, and town or village is identified as the implementation unit of CLULA. The plan for CLULA will be conducive to the concentrated farming of food crops according to the suitable natural conditions and management level. The research realized the optimization of spatial structure and cultivated land use patterns of different food crops integrating farming with protecting land. The significance of the study is that it provides a scientific basis and guidance for adjusting the regional planting structure and solving the problem of food structural imbalance.