N-hexadecanoylglycine (C16Gly) is a newly synthesized collector, which can be used as an efficient collector for fluorapatite (FA) rather than for dolomite. To extend our knowledge regarding the C16Gly collector, the contact angle method was employed to understand the flotation selectivity of C16Gly in the FA and dolomite system. On the other hand, the possible binding models of C16Gly anion on Ca-rich and PO4-rich terminations of FA (001) surface were investigated with density functional theory calculations to reveal the interaction between the C16Gly and the FA surface. Results showed that C16Gly anion could interact with these two terminations to generate 12 low-energy configurations, including bidentate, tridentate and chelating binding models. The C16Gly anion preferred to adsorb onto the Ca-rich termination, which is caused by the weaker electrostatic repulsion force between the C16Gly anion and the PO4 groups on this termination. The adsorption of C16Gly on these terminations was more stable than that on the dolomite (104) surface, which is one of the reasons for the preferential flotation of FA from dolomite using C16Gly as a collector. These findings provide further insights into the selectivity of C16Gly during the flotation of FA and dolomite.