Advanced oxidation processes (AOPs) are promising for the treatment of secondary swine wastewater effluents, however, the molecular-level understanding of effluent organic matter (EfOM) removal and transformation during AOPs is limited. This study employed molecular-level characterization based on Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and bulk characterizations to investigate these processes in various AOPs, including Cu-Fenton, UV-Cu-Fenton, Fenton, UV-Fenton, and UV/H2O2 treatments. Our findings revealed that the removal rates of dissolved organic carbon and EfOM molecules follow the sequence of UV-Fenton > Fenton > UV-Cu-Fenton > UV/H2O2 > Cu-Fenton, correlating with the rates of H2O2 decomposition during reactions. AOPs with faster H2O2 decomposition, indicative of higher reactive oxygen species generation, predominantly mineralize rather than transform EfOM. Linkage analysis highlighted oxygen addition and deamination as the primary transformation reactions, with variations in the dominance levels of these reactions across different AOPs. Recalcitrant molecule, particularly CHNO and CHO types, including low-molecular-weight carboxyl-rich alicyclic molecules, pose challenges in treatment. To enhance the efficacy of secondary effluent treatment, strategies focusing on the targeted removal of such recalcitrant EfOM should be developed. This study provided new insights into the selection and optimization of AOPs for secondary swine wastewater effluent treatment.