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Simple Summary: Any abnormalities in the physical properties of an egg can decrease the hatching rate. The embryos of oviparous reptiles obtain Ca from the eggshell. This motivated us to analyze the microstructure and Ca in the eggshells of Chinese alligators. We found that the shells of the eggs with high hatching rates were thicker than those of the eggs with low hatching rates. There were also fewer erosion-crater pores on the surfaces of the eggs with high hatching rates than on the surfaces of the eggs with low hatching rates. Moreover, the shells' Ca contents were significantly higher in the eggs with high hatching rates than in the eggs with low hatching rates. Cluster modeling indicated that the highest hatching rate occurred when the eggshell thickness was 200–380 µm and there were 1–12 pores. These results suggest that eggs with adequate Ca contents, thicker shells, and less air permeability are more likely to hatch. Furthermore, our findings can inform future studies. The Chinese alligator (Alligator sinensis), found only in a small region in southeastern Anhui Province, is listed as critically endangered (CR) by the International Union for Conservation of Nature (IUCN) due to its current declining population trend. Any abnormalities in the physical properties of an egg can decrease the hatching rate. In particular, eggshells play an essential role in embryo development, motivating us to analyze the microstructures of the eggshells of Chinese alligators. In this study, we categorized the eggshells into two groups, based on the hatching rates, and analyzed the relationship between the eggshell parameters (eggshell thickness, calcium content, and number of pores in erosion craters) and the hatching rate, as well as the relationships between the eggshell parameters. We found that the shells of the eggs with high hatching rates were thicker than those of the eggs with low hatching rates. There were also fewer erosion-crater pores on the surfaces of the eggs with high hatching rates than on the surfaces of the eggs with low hatching rates. Moreover, the shell Ca content was significantly higher in the eggs with high hatching rates than in the eggs with low hatching rates. Cluster modeling indicated that the highest hatching rate occurred when the eggshell thickness was 200–380 µm and there were 1–12 pores. These results suggest that eggs with adequate Ca contents, thicker shells, and less air permeability are more likely to hatch. Furthermore, our findings can inform future studies, which will be vital for the survival of the critically endangered Chinese alligator species. [ABSTRACT FROM AUTHOR]