A quantitative structure activity relationship (QSAR) model was developed to predict the degradation of pharmaceuticals during electro-peroxone (E-peroxone) process. Mechanisms for pharmaceuticals removal include electrolysis, ozonation and hydroxyl radical ((OH)-O-center dot) degradation processes. Thirty-six molecular descriptors were calculated and fifteen were determined to have a relatively close relationship with the enhancement efficiency which is measured by a synergistic enhancement factor. A principal component analysis was applied to reduce the dimensionality of the established model. A QSAR model was built using multiple linear regression (MLR) analysis. Based on this model, the significance of top three selected molecular descriptors are as follows: carboxylic acid group (similar to 46%), double bond equivalence (similar to 37%), energy gap between E-LUMO and E-HOMO (similar to 13%). These contributors confirm that % OH mechanism plays an important role in the E-peroxone process. This model had an R square value of 0.804. The correlation coefficients of internal and external validation of the model were 0.721 and 0.692 respectively.