An eccentric error compensation method is presented for the pitch deviation measurement of gears. The eccentric error compensation method mainly consists of the evaluation of the assembly accuracy, the reconstruction of the reference curve and the coordinate compensation of intersection points. The geometrical model of the measurement system was analyzed and the corresponding mathematical model was proposed. A gear with small modulus was adopted as the specimen for the pitch deviation measurement. Experimental results reveal that the values of eccentricity can be extracted from the measured profile successfully and the eccentric error compensation is effective for the pitch deviation measurement of gears.