There is provided a cleaning method of a film forming apparatus in which a process of forming a silicon film, a germanium film or a silicon germanium film on a substrate mounted on a substrate holder in a processing container is performed, comprising: etching away the silicon film, the germanium film or the silicon germanium film adhered to an interior of the processing container including the substrate holder by supplying a halogen-containing gas not containing fluorine into the processing container in a state where the substrate holder, which was stored in a dew point-controlled atmosphere after the film forming process, is accommodated in the processing container with no substrate being mounted thereon.