A system includes a multi-stage cryocooler having multiple stages and a temperature control system configured to regulate temperatures of the multiple stages of the multi-stage cryocooler. The temperature control system includes an input interface configured to receive (i) temperature setpoints for the stages of the multi-stage cryocooler and (ii) temperature information corresponding to temperatures measured at the stages of the multi-stage cryocooler. The temperature control system also includes processing circuitry configured to determine temperature errors and calculate at least one of a compressor stroke error and a pressure-volume phase error. The temperature control system further includes at least one controller configured to adjust at least one of a compressor setting and a pressure-volume phase of the multi-stage cryocooler.