The effects of C/N ratio of a nitrate-containing wastewater on nitrate removal performed by autohydrogenotrophic bacteria as well as on the morphological parameters of floc such as floc morphology, floc number distribution, mean particle size (MPS), aspect ratio and transparency were examined in this study. The results showed that the nitrate reduction rate increased with increasing C/N ratio from 0.5 to 10 and that the nitrogen removal of up to 95% was found at the C/N ratios of higher than 5 (between 0.5–10). Besides, high C/N ratio values reflected a corresponding high nitrite accumulation after 12-hr operation, and a fast decreasing rate of nitrite in the rest of operational time. The final pH values increased with the C/N ratio increasing from 0.5 to 2.5, but decreased with the C/N ratio increasing from 2.5 to 10. There were no significant changes in floc morphology with the MPSs ranging from 35 to 40 μm. Small and medium-sized flocs were dominant in the sludge suspension, and the number of flocs increased with the increasing C/N ratios. Furthermore, the highest apparent frequency of 10% was observed at aspect ratios of 0.5 and 0.6, while the transparency of flocs changed from 0.1 to 0.7.