Emerging pollutants in the form of pharmaceuticals have drawn international attention during the past few decades. Ciprofloxacin (CIP) is a common drug widely found in effluents from hospitals, industrial and different wastewater treatment plants, as well as rivers. In this work, the lab-scale 3D-BER system was established, and more than 90% of the antibiotic CIP was removed from Low C/N wastewater. The best results were obtained with the current intensity being taken into account, and a different C/N ratio significantly improved the removal of CIP and nitrates when the ideal conditions were C/N = 1.5–3.5, pH = 7.0–7.5 and I = 60 mA. The highest removal efficiency occurred when CIP = 94.2%, NO₃⁻-N = 95.5% and total nitrogen (TN) = 84.3%, respectively. In this novel system, the autotrophic-heterotrophic denitrifying bacteria played a vital role in the removal of CIP and an enhanced denitrification process. Thus, autotrophic denitrifying bacteria uses CO₂ and H₂ as carbon sources to reduce nitrates to N₂. This system has the assortment and prosperous community revealed at the current intensity of 60 mA, and the analysis of bacterial community structure in effluent samples fluctuates under different conditions of C/N ratios. Based on the results of LC-MS/MS analysis, the intermediate products were proposed after efficient biodegradation of CIP. The microbial community on biodegrading was mostly found at phylum, and the class level was dominantly responsible for the NO₃⁻-N and biodegradation of CIP. This work can provide some new insights towards the biodegradation of CIP and the efficient removal of nitrates from low C/N wastewater treatment through the novel 3D-BER system.