A substrate cleaning apparatus, includes a vaporizer configured to generate water vapor, a first heating part configured to heat a nitrogen gas to a first temperature, a second heating part configured to heat the nitrogen gas to a second temperature, wherein the second temperature is higher than the first temperature, and at least one cleaning chamber connected to the vaporizer, the first heating part, and the second heating part, wherein the at least one cleaning chamber is configured so that at least one substrate is exposed to the water vapor, the nitrogen gas having the first temperature, or the nitrogen gas having the second temperature under an atmospheric pressure.