Based on the lock-in photon-counting technique, a multi-wavelength single pixel spatial frequency domain imaging (SFDI) parallel detection system is proposed. With a digital micro-mirror device (DMD) as the modulated light source of diffuse reflected light to be measured under different wavelengths and another DMD as the equipment for the acquisition, coding, and convergence of diffuse reflection light, the converged diffuse reflected light is demodulated separately under different wavelengths based on the lock-in photon-counting technique, and simultaneously the cost of the proposed system is reduced. The time consumption of single-pixel imaging caused by multiple spatial encoding is effectively compensated via the introduction of the compressed sensing theory. The experimental results show that the proposed SFDI system can realize the reconstruction of diffuse reflection light from phantom surfaces under multiple wavelengths by encoding with only 20% of total pixels.