The flotation separation of rare earth minerals from calcium-bearing gangue minerals, such as calcite, remains a critical technical challenge in rare earth ore beneficiation. This study focuses on a green depressant, carboxymethyl chitosan (CTS), for the flotation separation of bastnaesite, parisite, and calcite using sodium oleate (NaOL) as a collector. Through flotation tests, zeta potential measurements, Fourier transform infrared spectroscopy, wrap angle test, atomic force microscopy, and X-ray photoelectron spectroscopy, the study elucidates the selective depression and interfacial mechanism of CTS on bastnaesite, parisite, and calcite. Molecular dynamics simulations were employed to elucidate the adsorption mechanisms of CTS and NaOL at the three-phase interface. The results demonstrate that in the NaOL flotation system, when CTS functions as a depressant, the carboxyl groups (-COOH) in CTS molecules selectively chemisorb to calcium sites on the calcite surface, forming hydrophilic Ca(COOR) complexes that significantly suppress calcite floatability. In contrast, CTS exhibits only weak physical adsorption on bastnaesite surfaces, which does not interfere with NaOL collection. This differential adsorption behavior establishes CTS as an environmentally friendly green organic depressant capable of achieving the efficient separation of the three minerals.