Efficient and sustainable water use in agriculture, as viewed through the lens of water footprint analysis, plays a crucial role in enhancing regional food security and environmental sustainability. Focusing on the rice-wheat rotation system, a crop water footprint calculation model was developed based on water footprint theory. The model was applied to assess the efficiency of water use in the rice-wheat rotation system in Lianshui Irrigation District spanning from 1960 to 2019. The analysis revealed the temporal evolution and influencing factors of water use efficiency in this system. Results indicated that the generalized water system number was ranged from 0.50 to 0.76 over the study period with a multi-year average of 0.65, showing no significant overall trend. In contrast, the crop production water footprint exhibited a yearly average of 58.4m3/GJ, displaying a consistent decline. Specifically, the green water footprint accounted for 40.6%~80.4% of the overall water footprint, while the blue water footprint averaged 22.6m3/GJ. Meteorological factors, predominantly precipitation, significantly influenced both the broad water system number and crop water footprint. The study highlighted a negative correlation between crop production water footprint and agricultural inputs, as well as regional irrigation intensity. Factors such as agricultural mechanization and water-saving irrigation practices played a crucial role in shaping water use efficiency. Enhancing rainfall utilization and adopting advanced agricultural technologies were identified as effective strategies to optimize water resource management in agriculture. Findings from this research can offer valuable insights for developing regional agricultural water conservation standards.