The invention discloses a method for removing water and acid in biological oil, which includes utilizing a molecular distillation process to distill biological oil, remove distillate on the cold surface and collect residual liquid on the hot surface on conditions that the cold surface temperature ranges from -15 DEG C to 5 DEG C and the hot surface temperature ranges from 20 DEG C and 90 DEG C. By means of the molecular distillation technique, proper cold surface temperature, hot surface temperature and a distance between the cold surface and the hot surface are defined, water and acid components in biological oil are removed successfully, acidity and water contents of biological oil are reduced greatly, and coking of biological oil during water and acid removing processes is overcome, thereby greatly increasing calorific value and service level of biological oil, expanding utilization ways of biological oil, improving industrializing development of preparing liquid fuel through biomass pyrolyzation, and having significant meaning to build a sustainable energy system and protect ecological environment.