Beacon position drift error in long baseline acoustic positioning system is difficult to identify and estimate. The equivalence of clock synchronization error is analyzed in synchronous distance ranging system and the beacon drift error is analyzed in response distance ranging system. A single beacon location algorithm is proposed based on effective sound velocity correction. A long baseline positioning algorithm which can effectively identify the beacon drift error is put forward without acoustic environment information. The effective sound velocity distribution range is used to identify the beacon drift error. The fixed beacon position drift error is estimated and corrected with the fusion trajectory. Experiment results show that the algorithm improves the positioning accuracy and robustness of long baseline positioning system.