A temperature control apparatus for fuel cell system comprising: a fuel cell stack; a first cooling line configured to circulate a first coolant that passes via the fuel cell stack; a first pump disposed on the first cooling line and configured to pump the first coolant; a first radiator disposed on the first cooling line and configured to cool the first coolant; a plurality of power electronic parts; a second cooling line configured to circulate a second coolant that passes via the plurality of power electronic parts; a second pump disposed on the second cooling line and configured to pump the second coolant; a second radiator disposed on the second cooling line and configured to cool the second coolant; a cooling fan configured to blow exterior air to the first radiator and the second radiator; and a controller connected to the first pump, the second pump, and the cooling fan, characterized in that the controller is configured to: determine an RPM of the cooling fan based on a coolant temperature at an inlet of the fuel cell stack and a first exterior air temperature; determine a target cooling performance of the plurality of power electronic parts based on power consumptions of the plurality of power electronic parts; and determine an RPM of the second pump based on the target cooling performance of the plurality of power electronic parts, the RPM of the cooling fan, and a second exterior air temperature, wherein the second exterior air temperature is an exterior air temperature that is measured after the first exterior air temperature is measured. a fuel cell stack; a first cooling line configured to circulate a first coolant that passes via the fuel cell stack; a first pump disposed on the first cooling line and configured to pump the first coolant; a first radiator disposed on the first cooling line and configured to cool the first coolant; a plurality of power electronic parts; a second cooling line configured to circulate a second coolant that passes via the plurality of power electronic parts; a second pump disposed on the second cooling line and configured to pump the second coolant; a second radiator disposed on the second cooling line and configured to cool the second coolant; a cooling fan configured to blow exterior air to the first radiator and the second radiator; and a controller connected to the first pump, the second pump, and the cooling fan, characterized in that the controller is configured to: determine an RPM of the cooling fan based on a coolant temperature at an inlet of the fuel cell stack and a first exterior air temperature; determine a target cooling performance of the plurality of power electronic parts based on power consumptions of the plurality of power electronic parts; and determine an RPM of the second pump based on the target cooling performance of the plurality of power electronic parts, the RPM of the cooling fan, and a second exterior air temperature, wherein the second exterior air temperature is an exterior air temperature that is measured after the first exterior air temperature is measured. determine an RPM of the cooling fan based on a coolant temperature at an inlet of the fuel cell stack and a first exterior air temperature; determine a target cooling performance of the plurality of power electronic parts based on power consumptions of the plurality of power electronic parts; and determine an RPM of the second pump based on the target cooling performance of the plurality of power electronic parts, the RPM of the cooling fan, and a second exterior air temperature, wherein the second exterior air temperature is an exterior air temperature that is measured after the first exterior air temperature is measured.