A System and method to control the coolant temperature of two independent cooling loops of a fuel cell Vehicle by adjusting System pump Speed, fan Speed and radiator bypass valve position. Multiple feedback controllers coordinated by robust flip-flop logic are used, to minimize energy consumption and provide optimal control System performance even in the case of Substantially different plant responses with respect to fan Speed and valve position plant inputs. The System also includes a feed forward disturbance compensator, which reacts immediately to change in net power and vehicle Speed disturbance variables, thereby reducing the variance of the temperature control error. Additionally, a feedback controller preset Strategy is used to compensate for distinctive plant nonlinear effects Such as bypass valve dead-Zone and air-conditioning System's request for abrupt change of fan Speed.

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