The key security of quantum key distribution (QKD) is guaranteed by the basic principle of quantum mechanics, which makes it possible to combine information theory security communication with one-time encryption. The key is usually encoded on the polarization dimension or phase dimension of a single-photon. It is considered that the birefringence effect of single-mode fiber leads to a random variation of polarization state, which would induce the bit error rate. So it is of great significance to keep the single-photon linear polarization state stable for both polarization encoding QKD system and phase encoding QKD system. By using the single-photon polarization modulation technology, the single-photon linear polarization state periodically varies with the external modulation signal. The flicker noise is suppressed effectively, and the signal-to-noise ratio (SNR) of single-photon counting is increased as indicated by the phase-sensitive detection with a lock-in amplifier (LIA). The error signal is generated by demodulating the modulated single photons and it is used to lock an arbitrary 1550 nm single-photon linear polarization state to the optical axis of in-line polarizer (ILP). The modulation frequency reaches up to 5 kHz, which can eliminate the influence of low frequency flicker noise. The LIA demodulates the single-photon pulses by using 78.1 Hz filter bandwidth, with a time constant of 1 ms and a filter slope of 24 dB. The SNR of error signal is 20. The zero-crossing point of error signal represents the single photon’s linear polarization state aligned to the optical axis of ILP. The linear slope around the zero-crossing point for the polarization state angle versus the error signal amplitude is 1.267 rad/V. When the negative feedback loop does not work, the polarization drift of single-photon pulses is 0.082 rad due to the random environmental noise. However, by using the single-photon polarization modulation technology, the polarization drift of stable single-photon pulses is limited to 0.0011 rad within 2000 s through the precise control with a polarization rotator, and the corresponding Allan deviation reaches the minimal value of 6.7×10^–5 at an integration time of 128 ms. The advantages for the single-photon polarization modulation technology are as follows: i) the linear polarization state drift is compensated in real-time at the single-photon level; ii) single frequency polarization modulation can be extended to multiple frequency polarization modulation in order to achieve simultaneous locking of multiple linear polarization states of single-photon pulses; iii) these 1550 nm single-photon pulses with the 0.0011 rad linear polarization state stability can be directly used as the single-photon source in either polarization encoding or phase encoding QKD system.