In this study, mesoporous Fe/MCM-41 was prepared and employed as a heterogeneous Fenton catalyst for the oxidative degradation of dye rhodamine B (RhB) in aqueous solution. Structural and morphological characterizations were performed using XRD, BET, FTIR, and SEM-EDX techniques. Fe/MCM-41 exhibits high catalytic activity for degradation of RhB in the Fenton-like system consisting of solid catalyst and H2O2. ·OH radicals were demonstrated to be the dominant active species by using tert-butanol as a probe compound. It was suggested that dye adsorption and ·OH generation are independent of each other during the heterogeneous Fenton process at the studied initial dye and H2O2 concentrations. The intermediates of RhB degradation were identified by LC-MS technique in this study. It can be inferred that the destructions of the conjugated structure and N-de-ethylation happen simultaneously during the heterogeneous Fenton process.