An integrated vertical-flow constructed wetland-microbial fuel cell system (CW-MFC), consisting of an up-flow chamber and a down-flow chamber, was constructed to treat synthetic sewage wastewater. The performance of CW-MFCs filled with different substrates [i.e., ceramsite (CM-A), quartz (CM-B), and zeolite (CM-C) granules] under various hydraulic retention times (HRTs, 7.6, 4.0, and 2.8 d) was evaluated. Efficient and stable nitrogen (N) and phosphorus (P) removals were observed in CM-A under different HRTs, while the voltage outputs of the CW-MFCs was greatly reduced as the HRTs decreased. With an HRT of 2.8 d, the ammonium (NH
4
+
-N) and orthophosphate (PO
4
3–
-P) removal efficiencies in CM-A were as high as 93.8 and 99.6%, respectively. Bacterial community analysis indicates that the N removal in the cathode area of CM-A could potentially benefit from the appearance of nitrifying bacteria (e.g.,
Nitrosomonas
and
Nitrospira
) and relatively high abundance of denitrifiers involved in simultaneous nitrification and denitrification (e.g.,
Hydrogenophaga
,
Zoogloea
, and
Dechloromonas
) and denitrifying sulfide removal (e.g.,
Thauera
). Additionally, the difference in N removal efficiency among the CW-MFCs could be partly explained by higher iron (Fe) content in milled ceramsite granules and higher abundance of denitrifiers with nitrate reduction and ferrous ions oxidation capabilities in CM-A compared with that in CM-B and CM-C. Efficient PO
4
3–
-P removal in CM-A was mainly ascribed to substrate adsorption and denitrifying phosphorus (P) removal. Concerning the substantial purification performance in CM-A, ceramsite granules could be used to improve the nutrient removal efficiency in integrated vertical-flow CW-MFC.