According to one aspect of the technique, there is provided a method of manufacturing a semiconductor device, including: (a) heating a substrate to a first temperature while supporting the substrate on a substrate support, and supplying a process gas into a process vessel accommodating the substrate support; (b) lowering a temperature of a low temperature structure provided in the process vessel to a second temperature lower than the first temperature by supplying an inert gas or air to a coolant flow path provided in the process vessel after (a) for a predetermined time, wherein defects occur when a cleaning gas is supplied to the low temperature structure at the first temperature; and (c) cleaning the low temperature structure by supplying the cleaning gas into the process vessel after (b).