For efficient usage of visible light, Pd loading graphitic carbon nitride (Pd/g-C3N4) hybrids were synthesized and peroxymonosulfate (PMS) was accompanied to improve the photoactivities of Pd/g-C3N4. The photocatalytic system consisting of Pd/g-C3N4, PMS and visible light (Pd/g-C3N4-PMS-Vis) exhibited higher bezafibrate (BZF) removal efficiency than Pd/g-C3N4-PMS, Pd/g-C3N4-Vis, g-C3N4-PMS, g-C3N4-Vis, and g-C3N4-PMS-Vis systems, which can be ascribed to the electron transfer from Pd/g-C3N4 to PMS. Density functional theory (DFT) calculation proved that the chemical bond interaction forming between Pd and g-C3N4 inspired the electron excitation, separation and transportation. Meanwhile, Pd particles with local surface plasma resonance (LSPR) phenomenon could also enhance the visible light adsorption. Notably, the photocurrent response of Pd/g-C3N4 was significantly improved with PMS, demonstrating the photoinduced electrons on Pd/g-C3N4 are capable to immigrate to PMS. The added PMS can perform as electron acceptors, thus favoring the quantum efficiency of photoinduced charge carriers to form SO4−. The BZF degradation mechanism was clarified by the addition of different scavengers and the major reaction active species were hydroxyl radicals (OH) and sulfate radical (SO4−). Four possible pathways in the degradation of BZF were also put forward via LC-MS/MS analysis (R-oxy substituent, oxidation dichlorination, OH-addition and oxidation deaminization). In the 2%Pd/g-C3N4-PMS-Vis system, an obvious decrease of genetic toxicity was observed because of the high removal efficiency and final low concentration of BZF. The results of this research underlined great prospective of Pd/g-C3N4 catalysts and provided a potential approach to photocatalytically remedy the polluted water by micropollutants.