A method was proposed where an active phase shifter with acoustic power recovery was applied to actively control their cooling supplies there in response to the new requirement of variable cooling supplies in dual temperature zones in space exploration. The influence characteristics on the distribution of the cold finger acoustic power and the efficiency of the regenerator in the dual temperature zones were obtained by analyzing the influence of the piston movement characteristics of the phase shifter in the high-temperature zone on the impedance of the cold fingers in the dual-temperature zones. The cryocooler can actively supply the desired cooling powers (@80 K and 40 K), respectively. The numerical calculation results show that the phase difference of the phase shifter piston mainly influences the cooling capacity in the high-temperature zone. The amplitude and phase difference of the phase shifter piston significantly affects the cooling capacity in the low-temperature zone. The experimental results show that the cooling capacity in the 80 K temperature zone can be actively adjusted in the range of 9.2 W to 23.7 W with the active control of the phase shifter, and the cooling capacity in the 40 K temperature zone can be actively adjusted in the range of 3.2 W to 4.5 W.