The Stirling/pulse tube cryocooler (SPC) is one of the most promising cryocoolers for space applications due to its advantages like high efficiency and long lifetime. The second pulse tube stage is coaxial pneumatically coupled in series with the first Stirling stage. The SPC possesses a distinctive capability to dynamically adjust the inter-stage refrigeration capacity by actively controlling the Stirling displacer in the first stage. This enables the SPC to effectively cater to varying heat loads over time. Nevertheless, the investigation into the regulation mechanism of the second-stage phase shifter on inter-stage refrigeration capacity shift is hindered by the presence of the second-stage passive phase shifter. This manuscript proposes an SPC with a second-stage active phase shifter (APS), which can actively control the phase difference between the pressure wave and mass flow at the second-stage hot end of the pulse tube in real time. The effect of the APS phase and amplitude on the inter-stage refrigeration capacity shift is analyzed using the theoretical and numerical model proven by the experiment. The first experimentally reported SPC with a second-stage APS demonstrates a refrigeration capacity of 0.22 W at 20 K plus 3.11 W at 70 K, requiring a compressor electrical power of 220 W. The SPC achieves a no-load minimum temperature of 13.5 K.