The deposal of residual hydrogen peroxide (HO) in Fenton-like system and the requirement of oxygen in bioreactor are essential parts for the treatment of integrative Fenton-like/bioreactor. A novel low-cost integrative Fenton-like and MnO-filled upward flow biological filter bed (Fenton-like/MBFB) equipped with the modified ceramsite was constructed to evaluate the main properties and catalytic activity of modified ceramsite, and the optimal conditions of integrative system and compare integrative and traditional systems. In this study, the Fenton-like reactor with modified ceramsite had higher catalytic ability whose Acid Orange 7 (AO7) degradation efficiency reached to 79.3% due to large surface area and high porosity, compared with that with raw ceramsite (44.3%). Furthermore, total utilization efficiency of HO in integrative system (from 32.41% to 53.51%) and removal efficiencies of COD and AO7 were remarkably improved, which would effectively decrease the waste of HO and the setting of regulation pool and aeration tank. Thus, the integrative system can save 0.51 CNY/m in construction cost and 0.21 CNY/m in operating cost. The average COD removal efficiency, AO7 degradation efficiency and effluent DO concentration were achieved to 64.8%, 79.5% and 9.3 mg/L respectively in integrative system were achieved in integrative system during sixty successive runs. Also, the potential degradation pathway of contaminants was also proposed according to the [rad]OH-enhanced at Fenton-like reactor due to catalyst and adsorption of modified ceramsite and the removal of microorganisms and modified ceramsite for contaminants at MBFB. This study demonstrated the feasibility of integrative Fenton-like/MBFB filled with modified ceramsite for simultaneously decreasing operational cost and complexity and enhancing removal efficiency, thus provided a one-step alternative for refractory dye wastewater.