The traditional temperature modeling method is based on the full heating of the accelerometer to achieve thermal balance, which is not suitable for the cold start-up phase of the micro-accelerometer. For decreasing the complex temperature drift of the cold start-up phase, a new temperature compensation method based on a high-order Fourier transform combined model is proposed. The system structure and repeatability test of the micro digital quartz flexible accelerometer are provided at first. Additionally, we analyzed where the complex temperature drift of the cold start-up phase comes from based on the system structure and repeatability test. Secondly, a high-order temperature compensation model combined with K-means clustering and the symbiotic organisms search (SOS) algorithm is established with repeatability test data as training data. To verify the proposed temperature compensation model, a test platform was built to transmit the measured values before and after compensation with the proposed Fourier-related model and the other time-related model, which is also a model aiming at temperature compensation in the cold start-up phase. The experimental results indicate that the proposed method achieves better compensation accuracy compared with the traditional temperature compensation methods and the time-related compensation model. Furthermore, the compensation for the cold start-up phase has no effect on the original accuracy over the whole temperature range. The stability of the accelerometer can be significantly improved to about 30 μg in the start-up phase of different temperatures after compensation.