The invention discloses a method and a system for controlling secondary water supply chlorination in a complex loop. The method comprises the steps of adding a sodium hypochlorite solution as a disinfectant to water in a water tank for disinfection, wherein the initial default adding coefficient is k1, the disinfectant is proportionally added according to the inflow rate Q1, and the adding amountQ2 is equal to k1Q1; after t1 time, adjusting the adding coefficient k according to the residual chlorine concentration signal of the effluent fed back from the water outlet of the water tank, whereink is equal to k1-k2, the adjustment time is t2, and k2 is the adding coefficient that needs to be adjusted; and when the residual chlorine concentration of the effluent fed back from the water outletdoes not reach a set value, refilling the disinfectant to the water tank, wherein the refilling amount V is equal to vk2, and v is the volume of water in the tank. The method and the system achieve chlorination disinfection on the water in the secondary water supply tank, and the equipment is intensive, efficient, simple and convenient; the whole equipment is fully automatic, the adding amount ofthe reagent is continuously analyzed and adjusted through the residual chlorine concentration of the effluent, thereby avoiding inaccurate adding amount caused by the concentration change of the reagent, and prolonging the changing cycle.