The comprehensive reform of agricultural water price (CRAWP) applies the modern water management concept of government-market-society combination to improve agricultural water efficiency and ensure national water security. This study systematically examined the evolution process and internal logic of the CRAWP policy, identified the practical difficulties, clarified the deepening direction, and put forward countermeasures for the future. Results show that China’s CRAWP policy has gone through four stages: the exploration period, the pilot period, the comprehensive promotion period, and the breaking through period. The evolution path of the CRAWP indicated that the objectives and directions have been continuously clarified, the tasks have been deepened from a single breakthrough to the whole chain, and the measures have been constantly diversified. The internal logic of the evolution path of the CRAWP was based on the complexity of the reform objects and the priority was different in different stages. Based on the current situation of farmland water conservancy, the reform took the path of “building mechanism first and then engineering”. Based on the basic agricultural conditions, the reform must simultaneously design the reward and compensation mechanism. However, current CRAWP faced multiple practical dilemmas, including the large gap in capital investment, the low enthusiasm of local and rural households to participate, the absence of the “main body” of end-use water management, and the regional imbalance in the reform process. In the future, the deepening direction of the CRAWP includes further optimizing the water price structure, establishing a reasonable water price sharing, accurate pricing, and subsidy mechanisms, and improving the reform of water right system. This paper also suggests: thoroughly studying water price forming mechanism, incorporating farmland water conservancy into the construction of high-standard farmland, including precision subsidies and water-saving incentives into the comprehensive subsidy system for agricultural production, establishing a diversified management and maintenance mechanism through innovative government purchase services, and formulating a sub-regional acceptance criteria for the CRAWP according to local conditions.