Abstract: In 2000, China launched a series of positive policies to promote agricultural development in Northeast China, thus causing a rapid expansion of the cropping scale and a change of cropping structure in the Songhua River Basin. It is important to reveal the changes in cropping structure in the Songhua River Basin to improve its future supply capacity, ensure national food security, and achieve the adjustment of food production. In this study, we selected the Songhua River Basin, a major grain-producing area in China, as the study area. Based on the normalized difference vegetation index (NDVI), enhanced vegetation index (EVI), and land surface water index (LSWI) from MODIS data, a decision tree model was constructed by combining the phenological periods of different crops. The results of crop extraction were verified using observed datasets, verification points selected in Google Earth, and statistical almanac data. The values of extraction accuracy for rice, maize, and soybean were 0.9090, 0.9026, and 0.8200, respectively, with a Kappa coefficient of 0.79 and an overall accuracy of 0.84. The crop types in the Songhua River Basin were dominated by maize and supplemented by rice and soybean, forming a crop pattern of “soybean in the north, maize in the south, and rice near rivers”. The entire crop planting area of the Songhua River Basin was in a state of continuous expansion from 2000 to 2020, with the total planting area increasing from 95 556.26 km² to 173 070.00 km², an increase of 81.12%. The planting area of rice, maize, and soybean increased by 24 911.36 km², 54 432.07 km², and 20 719.77 km², respectively. Overall, the proportion of the rice planting area to the total planting area increased by 8.56%, and those of maize and soybean increased by 16.86% and 0.39%, respectively. The planting areas of rice and maize increased significantly in most areas of the Songhua River Basin, and the rice expanded mainly in the areas near rivers. The planting area of soybean increased significantly in the eastern part of the northern part of the basin. The cities in the Songhua River Basin have formed a distinctive cropping structure, with most areas changing from a double-crop-dominant type to a maize-dominant type. In 2020, there was the addition of rice-dominant cities in the basin, the disappearance of maize-rice dominant cities and soybean-rice dominant cities, and the transformation of both maize-rice dominant cities and maize-soybean dominant cities into maize-dominant cities, with a gradual concentration of crop cropping types. The results of this study provide a scientific understanding of the adjustment of cropping structure and guidance of agricultural production in the Songhua River Basin.