The difference in chalcopyrite's primary ore-hosting rocks (dolomite and carbonaceous slate) in the Democratic Republic of the Congo results in an extremely uneven grain size distribution. Additionally, the presence of 2.21% organic carbon in the gangue impacts flotation efficiency. To address these challenges, ore properties were analyzed using the Mineral Liberation Analyzer (MLA), X-Ray Diffractometer (XRD), and microscopy. Flotation process was modified to incorporate a "middlings regrinding" processing, utilizing PDEC (an alkyne-based thioester collector, prop-2-yn-1-yl diethylcarbamodithioate) as the collector for experimental studies. Density Functional Theory (DFT) calculations elucidated the interaction mechanism of PDEC on chalcopyrite's surface. The MLA analysis indicates that chalcopyrite is mainly found in medium to fine grains, with the presence of fine-grained copper minerals smaller than 0.04mm accounting for 16.29% of the sample. This implies that these minerals require fine grinding for effective separation. Despite interference from organic carbon, PDEC demonstrates remarkable selectivity and efficiency in chalcopyrite flotation. By employing the "middlings regrinding" flotation method, a concentrate with a Cu content of 26.79% and a recovery of 87.88% was achieved, representing an increase of 0.17% in Cu grade and 4.09% in recovery rate compared to the conventional flotation process. DFT analysis demonstrates that the S 3p orbitals in carbon-sulfur double bond of PDEC and the C 2p orbitals in its acetylene group significantly affect its collection efficiency, engaging in hybridization with the Fe 3d orbitals on the surface of chalcopyrite, thereby facilitating a robust bonding interaction.