In this study, boron-doped polycrystalline diamond (BDD) films were deposited on 6-inch silicon wafer by using microwave plasma chemical vapor deposition (MPCVD). Mixed gas containing hydrogen, methane, and diborane was used as precursor and the wafer temperatures were set at 750 °C, 850 °C and 950 °C, respectively. Five-fold twin structures were observed in the samples prepared at 850 °C and they promote the increase of surface roughness. Furthermore, these twin structures may lead to the increase of boron atoms at the surface, which was verified by first-principles calculation. BDD film that contains five-fold twin structures has higher Hall mobility, lower electrical resistivity and larger hole carrier concentrations at room temperature. Besides, reactive red X-3B (200 mg/L) was fully degraded by BDD electrodes at current density of 100 mA/cm2 within 40 min using NaCl as supporting electrolyte. Overall, BDD film electrodes prepared by appropriate methods contain a large quantity of five-fold twin structures surface have excellent electrochemical properties and thereby demonstrate potential as a promising waste water degradation material.