In this study, reductive graphene oxides (rGO) and heteroatoms (N and P) doped graphene oxides (NGO, PGO) were synthesized and firstly applied in catalytic ozonation of sulfamethoxazole (SMX). As metal-free materials, NGO and PGO were found to exhibit significant abilities in catalytic ozonation of SMX, of which the efficiency were both more than 2.5 times to ozonation system and 1.5 times to the undoped rGO, respectively. Materials characterization showed the doping of heteroatoms into graphene oxides layers would modulate the configuration and properties of graphene oxides meanwhile create new active sites to enhance the catalytic performance. Density functional theory (DFT) calculations were then employed to give an in-depth probe of the degradation mechanism. The theoretical calculations were in good correspondence with the experimental results, indicating that the S atom was the most susceptible attacking site, which resulted in the cleavage of SN and SC bond of SMX during the catalytic ozonation processes. This study proposes a new insight into catalytic ozonation of SMX by NGO and PGO materials.