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Amelogenin is the main component of the organic matrix necessary to the formation of tooth enamel by directing the hydroxyapatite (HAP) growth. However, the detailed mechanism of adsorption between amelogenin and HAP is still not clear. In this report, simulations of the dynamic behavior of six different orientations of leucine-rich amelogenin protein (LRAP), the amelogenin splice variant, on a fixed hydrophilic HAP surface (001) were performed. Energy minimization, molecular dynamics (MD), and steered molecular dynamics (SMD) simulations were integrated in carrying this study. The results are highly consistent with the previous experimental findings. It was confirmed that the carboxyl groups contributed mainly to the adsorption of LRAP on the HAP (001) surface. Moreover, it was found that the −COO- claw of LRAP grasps the calcium ion with its two oxygen atoms in a special triangle form. This interaction form can resist external forces and is the key factor of the adsorption between LRAP and HAP.