Efficient and selective flotation separation of chalcopyrite and pyrite in copper-sulfur ores remains a challenging issue in mineral processing. In the present work, a newly-synthesized organic compound morpholine dithiocarbamate propylene ester (MDPE) was first developed as a flotation collector in the chalcopyrite-pyrite system. Microflotation results indicated that MDPE exhibited surpassing flotation selectivity for chalcopyrite against pyrite at low alkalinity (pH = 8.5) compared with traditional sodium isobutyl xanthate (SIBX) or sodium diethyldithiocarbamate (DTC). UV–vis spectra showed that MDPE was preferable to interact with Cu+ or Cu2+ rather than with Fe2+ or Fe3+. The results of zeta potential and FTIR spectra proved that MDPE had a stronger adsorption affinity towards chalcopyrite rather than pyrite. FTIR and XPS results confirmed that MDPE might chemically absorb on chalcopyrite surfaces by the formation of Cu-MDPE complexes with C-S-Cu structure.