BackgroundHigh grain breakage rate is the main limiting factor encountered in the mechanical harvest of maize grain. X-ray micro-computed tomography (μCT) scanning technology could be used to obtain the three-dimensional structure of maize grain. Currently, the effect of maize grain structure on the grain breakage rate, determined using X-ray μCT scanning technology, has not been reported. Therefore, the objectives of this study are: (i) to obtain the shape, geometry, and structural parameters related to the breakage rate using X-ray μCT scanning technology; (ii) to explore relationships between these parameters and grain breakage rate.ResultIn this study, 28 parameters were determined using X-ray μCT scanning technology. The maize breakage rate was mainly influenced by the grain specific surface area, subcutaneous cavity volume, sphericity, and density. In particular, the breakage rate was directly affected by the subcutaneous cavity volume and density. The maize variety with high density and low subcutaneous cavity volume had a low breakage rate. The specific surface area (r = 0.758*), embryo specific surface area (r = 0.927**), subcutaneous cavity volume ratio (0.581*), and subcutaneous cavity volume (0.589*) of maize grain significantly and positively correlated with breakage rate. The cavity specific surface area (− 0.628*) and grain density (− 0.934**) of maize grain significantly and negatively correlated with grain breakage rates. Grain shape (length, width, thickness, and aspect ratio) positively correlated with grain breakage rate but the correlation did not reach statistical significance. The susceptibility of grain breakage increased when kernel weight decreased (− 0.371), but the effect was not significant.ConclusionsThe results indicate that X-ray μCT scanning technology could be effectively used to evaluate maize grain breakage rate. X-ray μCT scanning technology provided a more precise and comprehensive acquisition method to evaluate the shape, geometry, and structure of maize grain. Thus, data gained by X-ray μCT can be used as a guideline for breeding resistant breakage maize varieties. Grain density and subcutaneous cavity volume are two of the most important factors affecting grain breakage rate. Grain density, in particular, plays a vital role in grain breakage and this parameter can be used to predict the breakage rate of maize varieties.