China is currently experiencing severe water scarcity issues in its agricultural production sector. To address this challenge, the Chinese government has taken steps towards implementing a nationwide reform in agricultural water pricing to accelerate the more sustainable management of the agricultural water resources sector. The present study adopted a multiple regression model to test four alternative irrigation water charging methodologies (charges based on ladder pricing, time, land area, and electricity) accompanied by supportive agricultural pricing policies to address the inherent conflicts between water conservation and agricultural development goals. This study focused on the Wei River Basin, which is recognized as a highly water-stressed region in China. This basin was chosen as a pilot area for comprehensive reform initiatives related to agricultural water pricing and served as the geographical scope for our research. Between June and July of 2022, we conducted comprehensive field surveys within the Wei River Basin, accumulating a dataset of 415 data points pertaining to the crop year of 2022. Our results showed that the ladder water price-based method exhibited remarkable potential in achieving substantial savings, with a minimum of 60.5239 m3/mu of irrigation water conserved for food crops and an impressive 67.8090 m3/mu for cash crops. However, regarding water-saving irrigation technologies, the estimation results indicated that electricity-based charging outperformed the other methods, resulting in an impressive 55.22% increase when ladder pricing served as the benchmark. In addition, regarding agricultural green production, the results for food crops and cash crops are different, with food crops being more sensitive to the ladder water price policies. Moreover, the results suggested that different water charging methods have significant heterogeneity effects from the perspective of the farmers’ scale, land fragmentation, and water price awareness capacity. This study forges an innovative path for water-stressed nations to execute agricultural water pricing reform and enhance agricultural production’s sustainable growth.