Functional near-infrared spectroscopy imaging has become the preferred choice as a neuroimaging technique of brain function research. To obtain the imaging system with high sensitivity, large dynamic range and high temporal resolution, we develop a multi-channel near-infrared brain functional imaging system based on improved lock-in photon-counting. The light source module consists of 16 laser diodes with wavelength of 785, 808 and 830 nm, respectively, which are modulated by square wave with frequency space of 252 Hz. The detection module includes nine photon counting photomultiplier tubes. This system combines the ultra-high sensitivity of the photon-counting technology with the simple parallelism of the digital lock-in detection based on square wave modulation mode, and system performance meets requirements. The linear correlation coefficient can reach 0.9989, cross talk between channels is negligible. The system has strong anti-interference ability and the ability to locate accurately.