A method of manufacturing a semiconductor device having a process for cleaning a semiconductor substrate after the semiconductor substrate is etched for patterning includes a first process of preparing the semiconductor substrate having a first temperature, a second process of setting the semiconductor substrate at a second temperature, a third process of etching the semiconductor substrate having the second temperature by etching liquid having a third temperature, a fourth process of cleaning the semiconductor substrate to which the etching liquid is adhered, by ultrapure water having a fourth temperature, wherein the second temperature is set at the range between the first and the third temperatures.