High-heat-flux heat removal is critical for the long-term safety of the high-power electronic device, while the precise and uniform temperature control is challenging due to various uncertainties. To this end, active disturbance rejection controller (ADRC), hybrid with feed-forward flow-rate/sub-cooling controller, is introduced for the temperature regulation of a multiple degree-of-freedom mechanically pumped two-phase loop. Based on the proposed experimental setup, the optimal references of sub-cooling and flow-rate are identified and used as the feed-forward law for auxiliary loop control, and ADRC is used in the primary loop to control the evaporator wall temperature. The experimental results indicate the efficiency of thermal control for the mechanically pumped two-phase loop via combination of primary and auxiliary loop. In addition, ADRC performs better in both temperature tracking and disturbance rejection when compared with the conventional PI controller, and its superiority consists in faster tracking and stronger robustness to disturbances and couplings.