Doppler estimation is a key link in the synchronization process of GMSK spread spectrum communication system receivers in the context of burst transmission. Given the extremely short information transmission time associated with short-duration burst GMSK spread spectrum communication systems, the synchronization segment structure of the system receiver is built. Based on this, a Doppler estimation algorithm adapted to the short-time burst synchronization segment structure is designed. The short-time burst Doppler estimation algorithm model is established. The algorithm formula is derived and the algorithm model is theoretically analyzed. The implementation process of the algorithm for Doppler estimation is described in detail, and the algorithm is simulated. The experimental results demonstrate that the Doppler estimation accuracy of the algorithm can reach 97.2% when the signal-to-noise ratio is 1 dB, and it exceeds 99% when the signal-to-noise ratio is greater than or equal to 3 dB. These findings validate the effectiveness and feasibility of the algorithm in GMSK spread spectrum communication systems within the context of burst transmission. It also shows that the Doppler estimation algorithm can still achieve superior accuracy even under weak signal conditions within the communication system.