The invention discloses a cleaning method of graphite base in MOCVD apparatus. The method is used for cleaning the graphite base in the MOCVD apparatus and can completely clean the graphite base cleanly, in particular the attachments in small pits on the surface of the graphite base without damaging the structure of the graphite base, so as to prolong the service life of the graphite base and improve the productivity of the MOCVD apparatus. The method comprises the steps of boiling in acid, specifically, putting the graphite base in phosphoric acid for boiling until the attachments on the surface of the graphite base are removed completely, then taking out the graphite base, and the step of boiling in acid further comprises the process of brushing off the attachments on the surface of thegraphite base; water-flushing, specifically, flushing the well boiled graphite base by hot de-ionized water to remove acidic substances on the graphite base; and drying, specifically, drying the graphite base until the graphite base thereon has no moisture. The drying step comprises the process of drying the graphite base in a roasting manner. The invention uses the way of wet treatment.