The invention relates to the technical field of photoelectric imaging detection, and particularly relates to a single photon imaging detector and a manufacturing method thereof. The manufacturing method comprises the following steps: a silicon substrate microchannel plate is manufactured, and a micro through hole array is arranged in the silicon substrate microchannel plate; a CMOS (Complementary Metal Oxide Semiconductor) imaging sensor array is manufactured; a photoelectric cathode is manufactured and tested in a packaging device, device wafer level structural integration is carried out on the silicon substrate microchannel plate, the CMOS imaging sensor array and the photoelectric cathode, the single photon imaging detector is formed, and the single photon imaging detector is tested. The wafer level packaging processing technology is adopted, the photoelectric cathode, the silicon substrate microchannel plate and the CMOS imaging sensor array are directly coupled, and a high-flexibility, high-speed, high-resolution, low-cost, low-power consumption, high-frame frequency, no-cooling and compact-size single photon imaging detector.