To address the challenge of separating bastnaesite rare earth minerals from gangue minerals, this study independently synthesized a novel multi-polar group cationic surfactant,2,2-bis(hydroxymethyl)-N1,N1,N3,N3-tetramethyl-N1,N3-bis(3-tridecanamidopropyl)propane-1,3-diaminium bromide (HTTPD), as a collector. The flotation results showed that HTTPD could obtain REO grade of 69.71% and recovery of 89.33%, significantly outperforming conventional collectors and proving to be an excellent collector. Density functional theory (DFT) calculation displayed that two quaternary ammonium groups and –NH/OH polar groups were main active sites with strong reactivity. The quaternary ammonium groups of HTTPD strongly adsorbed on the bastnaesite surface through electrostatic attraction, thereby enhancing the flotation selectivity from calcite. The –NH/–OH polar groups adsorbed with bastnaesite by hydrogen bonding interaction. Multi-polar group synergistic adsorption, formed through electrostatic attraction and hydrogen bonding interaction, was the primary mechanism for the efficient separation of bastnaesite and calcite. This research not only provided new insight and theoretical guidance for the design and application of novel collectors but also promoted the efficient development and utilization of rare earth mineral resources.