The invention discloses an automatic sputum liquefying instrument and a sputum liquefying method thereof. According to the automatic sputum liquefying instrument and the sputum liquefying method thereof, in the using process, a moving arm and a mechanical arm are arranged, the moving arm is used for moving a pipette, the mechanical arm moves up and down to pump liquid, discharge the liquid and blowing and mixing the liquid uniformly, automatic sputum liquefying, sputum-culture automatic sample adding and automatic sputum liquidation liquid sub-packaging are achieved, the automatic sputum liquefying instrument can treat sixteen sputum samples within 30 min, working efficiency is improved greatly, and the instrument has the advantages that automatic operation and flux treatment are achieved, operation is easy, use is convenient, and cross contamination between the samples is avoided; direct contact can be avoided, so that the probability of personnel infection and cross-contamination of the samples is reduced, and sputum is treated fast, economically and easily. The urgent basic requirement of a clinical testing mechanism is met. The instrument is applicable to the field of medical instruments.