Provided are a method of manufacturing a semiconductor device and a substrate processing apparatus. The method includes forming a thin film having a predetermined thickness and a predetermined composition on the substrate, the thin film including a first element and a second element different from the first element, by repeating a cycle a plurality of times, the cycle including: (a) forming a first layer including the first element and having a thickness of several atomic layers or less on the substrate by supplying a gas containing the first element into a process vessel accommodating the substrate under a condition where a chemical vapor deposition (CVD) reaction is caused; and (b) forming a second layer including the first element and the second element by supplying a gas containing the second element into the process vessel to modify the first layer without saturating a modifying reaction of the first layer by the gas containing the second element.