The invention belongs to the field of optical measurement, relating to a multi-channel single photon counting measuring system based on digital lock phase de-multiplex. The system comprises a light source part, a measuring part, a digital-to-analogue conversion circuit, a digital circuit, a communication circuit and a computer, wherein the digital circuit outputs a digital sine to obtain a simulative sine wave through the digital-to-analogue conversion circuit, a laser modulator modulates the amplitude of a laser and couples a plurality of beams of modulated lasers with different frequencies into one beam to form into a light source of frequency division multiplexing, the light source irradiates an object to be measured, an emitted weak diffused light is captured by a single photon counting measurer, and an electric pulse is outputted through a circuit; and the digital lock phase arithmetic which is tightly combined with the single photon counting is realized by the digital circuit, and a mixed signal from different light resources is extracted in a separating way in a passageway of the measurer according to a preset parameter when receiving the electric pulse to obtain the intensity information of an emergent light which corresponds to each light source. The system shortens the measuring time, reduces the complexity thereof, improves the flexibility of the circuit, and reduces the measuring error.