The invention aims to provide a district air-conditioner distributed secondary pump system, which comprises refrigeration main engines 1, chilled water primary pumps 2, a water segregator 3, a water collector 4, and a profit and loss tube 5. According to the invention, in the two forms of an indirect connection 1 and an indirect connection 2, a chilled water secondary pumps 6, plate heat exchangers 7, user chilled water circulating pumps 8, and user tail end air processing devices 9 are mainly arranged on a user side; in the direct connection form, the chilled water secondary pumps 6, the user tail end air processing devices 9, and a bypass pipe 10 of a secondary pump suction inlet with a control valve are mainly arranged in the user side. The invention also provides a connecting form of distributively arranging the secondary pumps to a chilled water distribution system of each user building, and a corresponding operation control method. The system can well realize the hydraulic equilibrium of each paralleled loop circuit of a district cooling system transmission and distribution network, improves the operation efficiency of the secondary pumps, and greatly reduces the water pump energy consumption, thereby improving the energy efficiency ratio of the overall system, and increasing the safety of the overall district cooling system.