Provided are a semiconductor device defect inspection method and system thereof, with which predetermined hot spots are inspected using a SEM, and with which the frequency of defects occurring at the hot spot is estimated statistically and with reliability. An inspection point is designated in design data by the defect type. A plurality of pre-designated inspection points is selected by the defect type from the designated inspection points. The plurality of pre-designated inspection points by defect type thus selected are image captured by the inspection points. A defect ratio, which is a ratio of the plural inspection points which are image captured by the defect type to the plural defects detected, and a reliability interval of the defect ratio which is computed by the defect type is compared with a preset reference value. A defect type having a defect occurrence ratio which exceeds the reference value is derived.