Sulfamethoxazole (SMX), a typical sulfonamide antibiotic, is ubiquitous in secondary effluent and may pose undesirable effects on the aquatic ecosystem and human health. Constructed wetland (CW) is more and more applied in advanced sewage treatment, and the substrate plays an important role in removing pollutants. Manganese (Mn) ore has been widely concerned as a new type of substrate to remove pollutants in CW due to its high adsorption and redox properties. However, the removal mechanism of antibiotics by Mn ore CW is still unclear. In this study, Mn ore was selected as the substrate of a vertical flow constructed wetland (VFCW) while gravel substrate was selected as a control group, and the removal efficiencies of SMX in two VFCWs were investigated and compared. Experimental devices were layered as different regions, including anaerobic (0–32 cm), anoxic (32–64 cm) and aerobic (64–80 cm) zones, to examine the removal characteristics of SMX in different regions. And the removal mechanism of SMX was also explored by examining the adsorption and oxidation of Mn ore and the microbial degradation performance. The results showed that the final removal efficiency of SMX in CW filled with Mn ore substrate (M-CW) (48.4%) increased by 39.6%, compared with CW filled with gravel substrate (G-CW) (8.8%). According to the calculation of mass balance, the total loss of SMX caused by the oxidation of Mn ore and biodegradation accounted for 33.0% of the total SMX input in M-CW, the SMX loss caused by the biodegradation in G-CW accounted for 13.0%, and the substrate adsorption in M-CW and G-CW occupied 15.0% and 7.0% of the total SMX input, respectively. Mn(II) was formed during the oxidation of SMX by Mn(III, IV) and dissimilated Mn(III, IV) reduction by microorganisms in anaerobic environment (0–32 cm). Whereafter, the produced Mn(II) entered into the aerobic zone (64–80 cm) with the water flow and was re-oxidized into biogenic Mn oxides (BioMnOx) which had high adsorption and oxidation performance for SMX. Therefore, Mn ore could enhance SMX removal efficiency in anaerobic and aerobic zones by Mn redox process.