In our work, hot filament chemical vapor deposition (HFCVD) method was employed to fabricate microcrystalline and nanocrystalline diamond films using only hydrogen and methane as precursor. Different factors such as methane concentration, substrate temperature and reaction pressure were studied and it reveals that methane concentration is the major contribution on the morphology change. The resulted morphology of diamond films changed from microcrystalline to nanocrystalline when the methane concentration increased from 2% to 10%. Boron-doped microcrystalline and nanocrystalline diamond films were both used as anodes for the electrochemical degradation of human urine. They show comparable efficiency on the degradation of organic compounds on both electrodes, and while show a small difference on the oxidation of chlorine ions and ammonia ions. However, the nanocrystalline diamond anode shows a longer lifetime due to the lower surface roughness in comparison with the microcrystalline diamond anode. Herein, the nanocrystalline diamond anode is promising for the industrial applications in the electrochemical oxidation of wastewater in the future.