In nature, selective interactions between chiral amino acids and crystals are important for the formation of chiral biominerals and provide insight into the mysterious origin of homochirality. Here, we show that chiral amino acids with different hydrophilicities/hydrophobicities exhibit different chiral selectivity preferences in the dynamically growing gypsum [001] steps. Hydrophilic amino acids show a chiral selectivity preference for their d-isomers, whereas hydrophobic amino acids prefer their l-isomers. These differences in chiral recognition can be attributed to the different stereochemical matching between the hydrophilic and hydrophobic amino acids on the [001] steps of growing gypsum. These different chiral selectivities resulting from the amino acid hydrophilicity/hydrophobicity are confirmed by the experimental crystallization investigations from nano regulation on dynamic steps, to microscopic modification of gypsum morphology, and to macroscopic precipitation. Furthermore, as the hydrophilicity of amino acids increases, the disparity in chiral selection rises; conversely, the increase in the hydrophobicity of amino acids results in a decline in chiral selection. These insights improve our understanding of the interaction mechanism between amino acids and crystals and provide insights into the formation process of chiral biominerals and the origin of homochirality in nature.