A control apparatus of a heat exchanging system according to the invention, decreases a duty ratio of the heater pump after connecting an engine water passage to a heater water passage, shutting off a predetermined water passage portion of the heater water passage, and increasing a duty ratio of an engine pump when the controls for shutting off the predetermined water passage portion, connecting the engine water passage to the heater water passage, decreasing the duty ratio of the heater pump, and increasing the duty ratio of the engine pump, are requested to be executed.