The filling ratio (FR) of a carrier has an influence on the pollutant removal of the aerobic moving bed biofilm reactor (MBBR). However, the effect of the polyethylene (PE) carrier FR on the performance and microbial characteristics of the denitrifying MBBR for the treatment of wastewater treatment plant (WWTP) effluent has not been extensively studied. A bench-scale denitrifying MBBR was set up and operated with PE carrier FRs of 20%, 30%, 40%, and 50% for the degradation of chemical oxygen demand (COD) and nitrogen from WWTP effluent at 12 h hydraulic retention time (HRT). The nitrate removal rates with FRs of 20%, 30%, 40%, and 50% were 94.3 ± 3.9%, 87.7 ± 7.3%, 89.7 ± 11.6%, and 94.6 ± 4.0%, and the corresponding denitrification rates (rNO3--N) were 8.0 ± 5.6, 11.3 ± 4.6, 11.6 ± 4.6, and 10.0 ± 4.9 mg NO3−-N/L/d, respectively. Nitrous oxide reductase (nosZ) gene-based terminal restriction fragment length polymorphism (T-RFLP) analysis illustrated that the highest functional diversity (Shannon’s diversity index, H′) of biofilm microbial community was obtained at 30% FR. The quantitative polymerase chain reaction (qPCR) results indicated that the abundance of nitrate reductase (narG) and nosZ genes at 30% FR was significantly higher than that at 20% FR, and no significant changes were observed at 40% and 50% FRs. Thus, 30% FR was recommended as the optimal carrier FR for the denitrifying MBBR.