Hybrid rice seeds from sterile lines have displayed a new type of heavy chalkiness in the subtropical zone of China in recent years, which was named top-gray chalkiness, resulting in a lower quality of hybrid rice seeds in large-scale production. In this study, the morphological characteristics of the chalky hybrid rice seeds were investigated, the microscopic structures of their chalky parts observed, the α-amylase activit and relative nutrient content analyzed, and the germination indexe and microorganism populations of the chalky hybrid seeds determined. The results revealed that top-gray chalkiness in hybrid rice seeds originated from the top site of the grain, and that the chalky part was probably infected by bacteri and fungi to form a gray colo and which further resulted in a lower germination rat and germination potential. This observed chalkiness in rice seeds differed from the previously reported rice chalkiness categories both in the occurrence positio and color. Besides, the amylopectin content declined in the chalky par and the protein content in the chalky part increased as compared to the normal seeds. This research could provide technical support for the hybrid rice breeding enterprises during the breeding of hybrid rice seeds in large-scale production.