Provided is a thermal processing method of a microorganism that prevents aggregates from forming. A step S1 includes inoculating the microorganism into a medium and cultivating the microorganism. A step S2 includes acquiring a concentrate liquid of the microorganism by centrifugalizing the cultivated medium. A step S3 includes heating the concentrate liquid of the microorganism using vacuum vapor. In the step S3, the concentrate liquid of the microorganism is injected into a tank unit of a jacket tank (step S31), and a pressure of an inner space of the jacket unit of the jacket tank is reduced (step S32). After reducing the pressure of the inner space, the vacuum vapor is supplied into the inner space to increase a temperature of the concentrate liquid of the microorganism to a sterilization temperature (step S33). A step S34 includes maintaining the concentrate liquid of the microorganism at the sterilization temperature for a predetermined time using the vacuum vapor.本發明的課題在於提供一種可以防止凝聚物的形成之微生物的加熱處理方法。其包含:將微生物接種於培養基,來培養微生物(步驟S1);藉由將培養後的培養基以離心分離機施以離心分離,而取得微生物的濃縮液(步驟S2);使用真空蒸氣加熱微生物的濃縮液(步驟S3)。於步驟S3中,包含:將微生物的濃縮液投入於夾套槽桶的槽桶部(步驟S31);對夾套槽桶之外套部的內部空間進行減壓(步驟S32);內部空間減壓後,將真空蒸氣供給至內部空間,使微生物的濃縮液的溫度上昇至殺菌溫度(步驟S33);使用真空蒸氣將微生物的濃縮液在殺菌溫度下維持一預定時間(步驟S34)。S1‧‧‧培養製程S2‧‧‧濃縮製程S3‧‧‧加熱製程S31‧‧‧投入製程S32‧‧‧減壓製程S33‧‧‧溫度上昇製程S34‧‧‧溫度維持製程