Sodium hypochlorite (NaOCl) is a widely used cleaning reagent for membrane separation processes to recover membrane permeability; however, the competitive interactions of different chlorine species with fouling layers have not been adequately elucidated. In this work, we investigated the pH-dependent diffusion of the active chlorine species and reactions involved in the consequent dissociation and/or destruction of the fouling layers. The hypochlorite conductivity and dynamic diffusion tests showed that an increase in pH facilitated the uneven and fast diffusion of active chlorine via relaxing the matrix structure of the fouling layer. Under the synergetic effects of oxidation, hydrolysis and hydraulic shearing, the enhanced diffusion resulted in an uneven but massive removal of the foulants rather than a layer-by-layer dissociation, leading to a higher membrane cleaning efficiency. Sodium dodecyl sulfate (SDS), an anionic surfactant, was added into the cleaning solution to further validate the diffusion-dependent cleaning mechanisms. With a faster diffusion process aided by SDS, the cleaning efficiency was significantly improved. These findings provide new insight into the chemical cleaning mechanisms, which are of great importance to the optimisation of cleaning efficiency for various membrane-based processes.