A method for cleaning a substrate on which a silicon layer and a silicon germanium layer are formed and exposed, and method for fabricating a semiconductor device using the cleaning method are disclosed. The cleaning method comprises preparing a semiconductor substrate on which a silicon layer and a silicon germanium layer are formed and exposed; and performing a first cleaning sub-process that uses a first cleaning solution to remove a native oxide layer from the semiconductor substrate. The cleaning method further comprises performing a second cleaning sub-process on the semiconductor substrate after performing the first cleaning sub-process, wherein the second cleaning sub-process comprises using a second cleaning solution. In addition, the second cleaning solution comprises ammonium hydroxide (NH.sub.4OH), hydrogen peroxide (H.sub.2O.sub.2), and deionized water (H.sub.2O), and the second cleaning solution comprises at least 200 times more deionized water (H.sub.2O) than ammonium hydroxide (NH.sub.4OH) by volume.