In Fenton-like reactions, metal-doped catalysts generally have high catalytic activity, but their active sites are always randomly distributed, yielding electron transfer mechanisms between orbitals are difficult to explain. Herein, a CuFe2S3-C/N catalyst was synthesized to activate peroxydisulfate (PDS) for phenanthrene (PHE) degradation. The periodic structure of CuFe2S3 nanocrystals embedded in the C/N skeleton facilitated the cooperation of Fe, Cu, and S, resulting in a more effective degradation of PHE [i.e., maximum degradation rate of up to 93.5% (Initial PHE concentration: 1 mg/L)]. A phenanthrene degradation pathway was then proposed, and the dominant reactive oxygen species were proven to be •OH, SO4•-, 1O2 and O2•-. This pathway was elucidated using density functional theory (DFT) methods, and the negative adsorption energy (-2.05 eV) of S2O82- corresponding to a spontaneous adsorption process. The CuFe2S3 surface stretched the O-O bond from 1.306 to 1.433 Å, and the loss of electrons from the 2p bonding orbital of O atoms led to a lower energy barrier for O-O bond cleavage. Additionally, the electrons were transferred from part of the 3d orbitals of Cu and Fe atoms to the 2p orbital of O atoms in S2O82- and the electron donating capacity of the Cu atom was 3–7 times higher than that of the Fe atom, indicating that the Cu atoms dominated the PDS activation. This study expands on approaches that can be used to modify metal-doped materials to degrade phenanthrene and it contributes towards a clearer understanding of electron transfer mechanisms underlying PDS activation.