In order to alleviate membrane fouling and improve removal efficiency, a series of pretreatment technologies were applied to the ultrafiltration process. In this study, ClO2 was used as a pre-oxidation strategy for the ultrafiltration (UF) process. Humic acid (HA), sodium alginate (SA), and bovine serum albumin (BSA) were used as three typical organic model foulants, and the mixture of the three substances was used as a representation of simulated natural water. The dosages of ClO2 were 0.5, 1, 2, 4, and 8 mg/L, with 90 min pre-oxidation. The results showed that ClO2 pre-oxidation at low doses (1–2 mg/L) could alleviate the membrane flux decline caused by humus, polysaccharides, and simulated natural water, but had a limited alleviating effect on the irreversible resistance of the membrane. The interfacial free energy analysis showed that the interaction force between the membrane and the simulated natural water was also repulsive after the pre-oxidation, indicating that ClO2 pre-oxidation was an effective way to alleviate cake layer fouling by reducing the interaction between the foulant and the membrane. In addition, ClO2 oxidation activated the hidden functional groups in the raw water, resulting in an increase in the fluorescence value of humic analogs, but had a good removal effect on the fluorescence intensity of BSA. Furthermore, the membrane fouling fitting model showed that ClO2, at a low dose (1 mg/L), could change the mechanism of membrane fouling induced by simulated natural water from standard blocking and cake layer blocking to critical blocking. Overall, ClO2 pre-oxidation was an efficient pretreatment strategy for UF membrane fouling alleviation, especially for the fouling control of HA and SA at low dosages.