Based on the survey of farmers in Liuxihe River Basin of Guangdong Province, a binary and multinomial logistic model were established to explore the impact of agricultural water price incentive structures on the deviation between farmers’ water-saving cognition and water-saving behavior. The results showed that: (1) the agricultural water price incentive structures had significant negative impact on the deviation between farmers’ water-saving cognition and water-saving behavior; (2) from the perspective of different deviation types of farmers’ water-saving cognition and water-saving behavior, agricultural water price incentive structures had a significant positive impact on farmers’ behavioral deviation and strong consistency between farmers’ cognition and behavior, but had a negative impact on farmers’ cognition deviation. The results indicated that the more strong the incentive intensity of agricultural water price incentive structures, the farmers would be more encouraged to adopt water-saving behavior, but had limited impact on the cognition of farmers with week consistency between farmers’ cognition and behavior. Therefore, the agricultural water price incentive structures should be improved to increase their incentive intensity to encourage farmers to save irrigation water resources. Meanwhile, the water-pricing policy should be strengthened to disseminate to improve farmers’ cognition of water saving.