Disclosed are a substrate processing apparatus and a method of cleaning the apparatus. The apparatus includes a process chamber, a support unit in the process chamber and configured to support a substrate, and a gas injection unit in the process chamber. The gas injection unit includes a first injection portion configured to inject a source gas, a second injection portion facing the first injection portion and configured to inject a reaction gas that reacts with the source gas, and a third injection portion configured to inject a cleaning gas that removes a reactant produced from the source gas and the reaction gas.