A method evaluates a defect region of a semiconductor substrate based on C-V characteristics of a MOS structure formed on the semiconductor substrate, including determining a relationship between defect region and flat band voltage or fixed charge density by using a semiconductor substrate having a known defect region, under a heat treatment condition and a C-V characteristic evaluating condition identical to conditions for evaluating a defect region of a semiconductor substrate to be evaluated, determining a flat band voltage or a fixed charge density of the semiconductor substrate to be evaluated from C-V characteristics of a MOS structure formed on the semiconductor substrate to be evaluated, and identifying the defect region of the semiconductor substrate to be evaluated based on the relationship between defect region and flat band voltage or fixed charge density previously determined, whereby the defect region of the semiconductor substrate is evaluated.