The invention belongs to the technical field of biology, and particularly discloses a pretreatment method of epothilone B fermentation liquor. An inorganic salt is added into the fermentation liquor,so that resin and thalli are thoroughly separated, only the resin phase remains after the thalli are removed, the subsequent extract is reduced to 1/3 of the original mixture, an organic solvent for further extraction is saved, and impurities in the thalli are prevented from being introduced into the subsequent purifying process; and impurities with the retention time similar to that of epothiloneB are removed from the source. In addition, the separated resin phase does not need to be centrifuged or filtered by a plate frame and is directly loaded into a column without blocking a sieve plate,so that the column passing time is saved. According to the pretreatment method of the epothilone B fermentation liquor, the thalli and the resin are well separated, subsequent extraction steps are simplified, the usage amount of subsequent extraction organic solvents is reduced, the extraction efficiency and yield are improved, the universality is high, and the industrialization cost is low.