This research provides a comprehensive analysis of the spatiotemporal evolution of the regional cropping structure and its influencing factors. Using Landsat satellite images, field surveys, and yearbook data, we developed a planting structure extraction model employing the classification regression tree algorithm to obtain data on the major crop cultivation and structural characteristics of Alar reclamation from 1990 to 2023. A dynamic model and transfer matrix were used to analyze temporal changes, and a centroid migration model was used to study spatial changes in the cropping structure. Nonparametric mutation tests and through-traffic coefficient analysis were utilized to quantify the main driving factors influencing the cropping structure. During the period of 1990–2023, the cotton area in the Alar reclamation region expanded by 722.08 km², while the jujube exhibited an initial increase followed by a decrease in the same period. The primary reasons are linked to the cost of purchase, agricultural mechanization, and crop compatibility. In the Alar reclamation area, cotton, chili, and jujube are the primary cultivated crops. Cotton is mainly grown on the southern side of the Tarim River, while chili cultivation is concentrated on the northern bank of the river. Over the years, there has been a noticeable spatial complementarity in the distribution and density of rice and cotton crops in this region. In the Alar reclamation, the main factors influencing the change in cultivated land area are cotton price, agricultural machinery gross power, and population. Consequently, implementing measures such as providing planting subsidies and other policy incentives to enhance planting income can effectively stimulate farmers’ willingness to engage in planting activities.