In order to cost-effectively remove carbon (C), nitrogen (N) and phosphorus (P) from secondary effluent (SE), a lab-scale denitrifying filter (DF) for generating biogenic manganese oxides (BMOs) was constructed, and its influent was the mixture of real SE and secondary influent (SI).When NH+4-N in the influent rose to around 3.2 mg/L with the improvement of the SI ratio, the effluent COD, filtered total nitrogen (TN) and phosphorus (TP) were 7.80, 0.63 and 0.014 mg/L with the corresponding removal rate (CRR) of 84.72 %, 97.17 % and 95.15 %, resp.The refractory organics were oxidized and hydrolyzed to biodegradable organics, providing carbon source, and the residual organics were hardly further removed, owing to their extremely poor biodegradability.N was synergistically removed by denitrification coupled with partial-denitrification anammox (PDA), which was confirmed by the fact that the contribution rate of PDA to TN removal was 30.43 % and removing 1 mg TN actually consumed 2.02 mg COD.P was mainly removed by reacting with Mn2+ from the influent or BMOs reduction to form chem. precipitation (Mn3(PO4)2).The presence of the main functional bacteria (manganese oxidizing bacteria (MnOB), anammox, denitrifying and hydrolytic bacteria) and the main functional genes further explained the efficient C, N and P removal and clarified the advanced C, N and P removal mechanism.This novel technique removed C, N and P with extremely high efficiency, extremely low operational cost and no secondary pollution.