A control system for a machine is disclosed. The control system may have a pump, a low pressure reservoir, and at least one actuator connected to receive fluid pressurized by the pump and discharge fluid to the low pressure reservoir. The control system may also have a bypass passage situated to allow fluid to bypass the at least one actuator, and a warmup valve disposed within the bypass passage and being movable between a flow-passing position and a flow-blocking position. The control system may further have a hydraulic temperature sensor configured to generate a signal indicative of a temperature of the fluid, and a controller in communication with the pump, the warmup valve, and the hydraulic temperature sensor. The controller may be configured to move the warmup valve to the flow-passing position, fix a displacement position of the pump, and adjust an input speed of the pump in response to the signal.