Significance: Nacre exhibits outstanding mechanical performance, which results from coordinated deformation mechanisms synergistically working in characteristic microstructures at multiple length scales. A comprehensive understanding of crystal defects within aragonite is critical for discussing the deformation behavior of nacre on microstructure at the nanoscale through atomic scale. By integrating aberration-corrected transmission electron microscopy, crystallographic analysis, and theoretical calculations, we reveal various crystal defects within aragonite at atomic scale and discuss their potential effects on deformation. Our work will serve as cornerstones for modeling analysis and in-depth discussions on nanoscale deformation mechanisms within nacre. Additionally, these atomic-scale insights will benefit theoretical evaluation of the environmental effect on defect formation, enabling defect control in synthetic aragonite and designing of stronger and tougher bioengineering materials.