A defect inspection method for a wafer is provided. The wafer comprises a component pattern. The method comprises the following steps: providing a defect inspection apparatus for inspecting the defects on the wafer to obtain a defect distribution map; providing a photo mask, wherein the photo mask comprises a exposure pattern corresponding to the component pattern; and comparing the defect distribution map with the exposure pattern and dividing the defects in the defect distribution map into a first killer defect group and a first non-killer defect group according to their corresponding locations in the exposure pattern. In addition, a wafer defect inspection system applying the same method is also provided.