Provided are a method of manufacturing a semiconductor device and a substrate processing apparatus. The method includes: forming a first layer including a first element on a substrate by supplying a gas containing the first element; forming a second layer including first and second elements by supplying a gas containing the second element to modify the first layer; and forming a thin film having a predetermined thickness by setting the forming of the first layer and the forming of the second layer to one cycle and repeating the cycle at least once. Pressure, or pressure and a gas supply time in one process of the forming of the first layer and the forming of the second layer are controlled to be higher or longer, or lower or shorter than pressure, or pressure and a time in the one process when the thin film having a stoichiometric composition is formed.