Phytolith-occluded carbon (PhytOC) plays a pivotal role in long-term carbon sequestration and climate change mitigation. However, there is relatively limited knowledge regarding differences in PhytOC stability among various crops and cultivars, as well as the impact of environmental conditions (climate factors and soil properties) on its stability. While agricultural practices have traditionally prioritized yield optimization, less attention has been paid to enhancing carbon stability and accumulation alongside high productivity. To address these gaps, we collected samples from 28 wheat cultivars and 23 rice cultivars of 51 representative field sites across China. We conducted a comparative analysis of PhytOC stability by measuring silicon and leached carbon concentrations through a 5-week rapid dissolution experiment at 25 degrees C. A novel method for assessing PhytOC stability based on principal component analysis was developed, yielding a composite index of stability. Subsequently, we explored the correlation between PhytOC stability and environmental conditions, unveiling both direct and indirect relationships with biotic and abiotic factors. The results indicate that PhytOC in rice exhibited greater stability than in wheat, revealing significant inter-varietal differences and a degree of spatial heterogeneity within both crops. Furthermore, PhytOC stability in wheat was more responsive to environmental conditions than in rice, influenced by spatial distribution and climate factors, such as sunshine duration, temperature, ground surface temperature, relative humidity, and carbon dioxide concentration. In contrast, PhytOC stability in rice was primarily driven by varietal differences. In conclusion, this study provides an insight for promoting long-term carbon sequestration and climate change mitigation through proper crop production and environmental modifications.