Carbonate widely exist in wastewater and natural water. Here we proposed an efficient refractory organics degradation method for carbonate-containing wastewater via generating carbonate radical based on a photoelectrocatalytic TNA-MCF system. In the system, TiO2 nanotube arrays (TNA) and modified carbon felt (MCF) were used as photoanode and cathode, respectively. HCO3− was used as electrolyte. The results show that the system achieved 85.78% removal rate after 120 min in rhodamine B degradation, which is 30% higher than that using SO42− as electrolyte. The excellent performance is attributed to the strong oxidation of CO3− to organics, which originates from the reactions between HCO3− and hvb+ on TNA photoanode. It was also generated from the activation of HCO3− with H2O2 or O2− on MCF cathode. Moreover, the mechanism of CO3− formation and its efficient degradation of organics were investigated. These results demonstrate that this system has a potential application in refractory organics degradation.