A free-space quantum key distribution (QKD) system based on mobile equipment can provide an effective method to construct a real-time full-coverage multi-node network. However, the existing free-space QKD systems based on mobile devices encounter the challenge regarding the lack of stability caused by equipment disturbance. The robustness of the QKD polarization encoder against mobile device disturbance will be significant. Owing to the inevitable disturbance in practical applications, even the polarization-maintaining fiber (PMF) cannot maintain its polarization-maintaining characteristics well, which in turn affects the stability of some systems based on PMF. Therefore, in order to ensure that stable coding can be achieved under disturbances, we propose a two-way differential modulation mode, in which stable coding can still be achieved even under disturbances. At the same time, in order to verify the actual anti-disturbance characteristics of the mode, the polarization-modulated unit (PMU) with a two-way differential modulation mode is used in this study to generate four long-term stable polarization states subjected to the disturbances with a frequency of 200 Hz. At the same time, the PMU has a higher insertion loss, which makes the influence of crosstalk on the system more obvious. We also discuss two ways i.e. the time domain and frequency domain, to reduce the crosstalk which is caused by the imperfection of the device. The experiment is performed at a repetition frequency of 250 MHz, and a commercial avalanche single-photon detector is used to detect the system’s quantum bit error rate (QBER). Under the condition of no disturbance, the average QBER is 0.39% in 2 h. Then a vibration of approximately 200 Hz is used to simulate the practical disturbances, the average QBER is 0.36% in 2 h, and the fluctuation range of the QBER is only within 0.2%. We propose the first feasible encoding scheme in disturbed environments to ensure the long-term stability of the encoded polarization states, which is expected to be used in the multi-node expansion of the quantum network.