The invention discloses a biomimetic catalytic oxidation method of thiophene compound, characterized by the structure of the biomimetic catalyst of formula I and formula II, wherein, M is Fe, Co or Mn; R1 is NO2, NH2, Cl, F, SOH3 or H; R2 is NO2, NH2, Cl, F, SOH3 or H; R3 is NO2, NH2, Cl, F, SOH3 or H, R4 is NO2, NH2, Cl, F, SOH3 or H; and R5 is NO2, NH2, Cl, F, SOH3 or H. Due to the application of metal phthalocyanine compound and metal porphyrins as the catalyst, the invention has the benefits of transferring and activating oxygen molecule, and catalytic oxidating organics with high selectivity under a mild condition. The reaction system of the invention has low use level of the catalyst, reduced cost, low reaction temperature and reaction pressure, no oil corrosion, is friendly to environment, can be recycled, as well as can achieve deep desulfurization of oil product, without requiring any cooxidation agent.