Grain structure is an important characteristic of maize varieties, particularly in representing the grain filling and texture in some cases. But the effect of kernel positions on grain structures in maize still remained unclear. Clarifying the kernel position effects of grain structure is beneficial to comprehensively grasp the grain characteristics of maize ears, and provides a reference for the production, processing and variety improvement of maize. In this study, three grain types of maize cultivars were taken to clarify the kernel position effects, including Denghai 618 (DH618), KX3564, and Xianyu 335 (XY335), from Qitai, Xinjiang of Western China in 2018. Samples were selected at regular kernel intervals, where each ear was in an average of 12 grains. A total of 104 samples were scanned from the three varieties. The grain three-dimensional structures were reconstructed by imaging processing, such as segmentation, thresholding, and reconstruction, where more than 900 2D images were obtained in the different sections (X-Y, X-Z, and Y-Z) of grains using an X-ray micro-computed tomography (X-ray μCT). In addition to visualization, the grain structural parameters were also extracted, including the embryo, endosperm, subcutaneous cavity, embryo cavity, hard endosperm, soft endosperm, and endosperm cavity. The internal structure of grain was more accurately determined, especially on the cavity structure of grain, compared with the traditional manual and machine vision. The results showed that the effect of kernel position grain structure indicators on ear was different. Specifically, the volume of embryo, endosperm, and hard endosperm showed a linear downward trend from the base to the top of the ear, without considering the extreme grains at both sides of the ear. The range of each indicator on ear was 15.82-33.36, 180.15-296.50 and 87.13-166.00 mm3, respectively. The cavity volume of subcutaneous, embryo, and endosperm remained stable in the middle of the ear, significantly lower than those in the upper and lower parts, in the sequence endosperm cavity> subcutaneous cavity> the embryo cavity. The ratio of embryo to endosperm was basically stable among grains. The volume of soft endosperm and the ratio of hard endosperm to soft endosperm decreased gradually from the base to the top, but the slope was different. There was the same tendency of parameters at different kernel positions in three varieties, but there were differences in absolute value: the ratio of grain embryo to endosperm at different positions of the ear in DH618 was significantly higher than those in KX3564 and XY335. The ratio of hard to soft endosperm in XY335 was significantly larger than those in DH618 and KX3564. In terms of grain cavities, KX3564 had a higher proportion of subcutaneous cavities and XY335 had a higher proportion of endosperm cavities. The volume proportion of embryo, endosperm and subcutaneous cavity in maize grains of the three varieties was 9.27%, 89.87% and 0.86%, respectively. X-ray μCT technology provides a new method and idea for the study of maize grain characters. Kernel position has also played a significant role in the grain structure among different positions of the maize ear. The findings suggest that the sampling position should be considered when conducting kernel research, due mainly to the differences of grain structure in positions of the maize ear.