Accurately identifying and comprehensively managing the health of cropland systems is crucial for maintaining national food security. In this study, a more suitable framework for evaluating the health status of cropland systems in arid areas was constructed, and a systematic diagnosis of the health status of a cropland system in Xinjiang was conducted by increasing cropland stress and extending the VOR model to the VOR-S framework. The principal driving factors and spatiotemporal heterogeneity of cropland system health were investigated by using geographic detectors and GTWR models. The results showed the following: (1) From 2001 to 2023, the health level of the cropland system in Xinjiang fluctuated and increased. The proportion of areas with higher health levels (health levels I and II) in the cropland system increased from 45.84% in 2001 to 50.80% in 2023. The overall environment of the cropland system thus improved. (2) From 2001 to 2023, in terms of stress on the cropland system in Xinjiang, the overall level of HAI (human activity intensity) exhibited an upward trend, while the overall SEI (soil erosion intensity) significantly decreased, and WEI (wind erosion intensity) remained relatively stable. (3) The explanatory power of driving factors for cropland system health is ranked by order of magnitude as follows: annual precipitation (0.641) > annual average temperature (0.630) > population density (0.619) > nighttime lighting (0.446) > slope (0.313) > altitude (0.267). In addition, the combination of climate and human activity factors plays a dominant role in the spatial differentiation of cropland system health. The research results can provide scientific reference for cropland protection policies in arid areas.