The invention provides a quantum technology based alternating-current differential measurement system and method and belongs to the field of metering. The system comprises a bias-voltage generation unit, a PJVS, a tested system and conversion unit, a clock source, a first sampling unit, a second sampling unit, an FPGA (field programmable gate array) control unit and a PC upper machine; the clock resource is connected with the bias-voltage generation unit, the tested system and conversion unit and the FPGA control unit respectively and provides time-base frequency for the bias-voltage generation unit, the tested system and conversion unit and the FPGA control unit; the bias-voltage generation unit generates bias current for the PJVS and drives the PJVS to output needed waveforms; the bias-voltage generation unit provides trigger signals for the FPGA control unit; the PJVS is connected with the first sampling unit and the second sampling unit respectively; the tested system and conversion unit is connected with the first and second sampling units respectively; the FPGA control unit is connected with the first and second sampling units and the PC upper machine respectively.