Constructed wetlands (CWs) are a promising method to treat effluent from wastewater treatment plants (WWTPs). However, low carbon/nitrogen (C/N) ratios of the influent inhibit denitrification in CWs, resulting in poor nitrogen removal efficiency. Herein, we compared traditional (control), biochar (BC), and β-cyclodextrin-functionalized biochar (BC@β-CD) CW systems to investigate nitrogen removal from influent with low C/N ratios, and the mechanisms that enhance this process. The highest nitrogen removal rates were observed in the BC@β-CD group, with rates 45.89% and 42.48% higher than those of the control, accompanied by a 70.57% and 85.45% decrease in nitrous oxide release, when the C/N ratio decreased from 4 to 2, respectively. Metagenomic and enzymatic analyses indicated that BC@β-CD enhances nitrogen removal by coordinately promoting carbon metabolism and increasing denitrification enzyme activities, without affecting microbial species diversity in CWs. Structural equation modeling confirmed that the foremost advantages of BC@β-CD were effective electron generation and transportation resulting from increased activities of nicotinamide adenine dinucleotide (NADH) dehydrogenase and the electron transfer system (ETS), thereby strategically reallocating more carbon metabolic flow to support denitrification. Our results show that the application of BC@β-CD in CWs to optimize the reallocation of electrons from carbon metabolism is a feasible strategy to enhance denitrification under low C/N conditions.