The suitability evaluation of agricultural land at the regional scale is of great significance for protecting land and water resources and building sustainable agricultural systems. Based on climate, soil, topographical, and surface water resources, land suitability index (LSI) data for maize, rice, and soybeans are established using an analytical hierarchy process and matter element analysis (AHP–MEA) model in Jilin Province, China. The results show that there is a significant positive linear correlation between the LSI and the measured yield, which indicates that the model has an ideal effect and certain reference and extension significance. The main limiting factors for maize and soybean planting are pH, total nitrogen (TN), available phosphorus (AP), and soil texture, while water shortage limits rice planting. Different spatial structure optimization schemes for planting are established using the LSI and measured yield, along with economic indices. This study shows that the scheme that integrates policy and cost can make full use of land and water resources and promote the economic growth of agriculture. After optimization, the planting areas of maize, rice, and soybeans were 7.22, 2.44, and 0.71 million ha, respectively, representing an increase of 15.71 billion yuan over the agricultural GDP for the existing planting structure. It is expected that this study will provide a basis for follow-up studies on crop cultivation suitability.