Fresh Xiang lotus, the relative parameters of fresh lotus seeds affecting the precision of mechanical core removal were measured and analyzed. A model of the section circle of fresh lotus seed is obtained with the attributes of circle center coordinates, diameter and roundness error, according to the coordinate parameters of each contour point on the same circle of fresh lotus seed. The center coordinates of each section alone the axis of the lotus core are fitted with least square method. A linear equation of lotus geometry axis is established. The measurement model of coaxially error between lotus geometry axis and lotus core axis is developed. Furthermore, an accurate measurement of the contour parameters of each section of the fresh lotus seed is implemented with the coordinate measuring machine. Based on the obtained measurement model, the center, diameter and roundness error values of the fitting circle for each section can be calculated. The measured data shows that the roundness error of fresh lotus along the direction of the lotus core approximates the parabolic law The roundness error is minimal the maximum section circle and vice versa. The average value of the maximum section circle is 0.347 3 mm. Therefore, the contour near the maximum section is chosen as the positioning reference, in order to achieve optimal centering accuracy. Finally, the circle center data of five section fitting circles near the maximum section are selected, based on the proposed approach. An approximate geometric axis of the fresh lotus seed is fitted. The average coaxially error between the geometrical axis of lotus seed and the lotus core axis is 0.914 0 mm. It can be seen that the size of the punch should be at least 0.914 0 mm larger than the size of the lotus core, during the mechanical operation process. The measurement results provide a basic dataset for the development of the mechanical centering machine of the fresh lotus seed. The proposed method also provides a reference for the geometric center measurement of irregular objects, which have similar attribute to lotus seeds.