In the long-distance water supply system, the air tank can effectively protect the pump failure water hammer, but the large air tank will increase the investment. This paper analyzes the hydraulic transient process of the water supply system with air tanks, and proposes a joint protection method with an air tank behind the pump and air valves at the end of the pipeline. The function and coupling relationship of the air tank and air valves are clarified, the theoretical analysis system and numerical optimization framework of the joint protection layout scheme are constructed, and the potential hidden trouble conditions are discussed. A setting method of combined air valves is proposed to eliminate the possible water and gas problems in the pipeline. Combined with the actual project, the water hammer protection effects of different protection schemes are compared and analyzed. The results show that this joint protection scheme can effectively protect against water hammer damage, and greatly reduce the volume of the air tank compared to a single air tank protection.