Single photon modulation has been proposed to overcome the defects of the low signal-to-noise ratio(SNR)and slow process rate of photon counting. In this paper, we present the quantum theory of single photon modulation, and then experimentally investigate the modulation spectroscopy both in the time domain and frequency domain. It is found that the SNR reached 150 in approximately the MHz modulation bandwidth. Single photon modulation has been solved to overcome the defects of the low signal-to-noise ratio (SNR) and slow process rate of photon counting. In this paper, we present the quantum theory of single photon modulation, and then experimentally investigate the modulation spectroscopy both in the time domain and frequency domain. It is found that the SNR reached 150 in approximately the MHz modulation bandwidth.