In this study, the common agricultural wastes (wheat straw, apricot pit and walnut shell) were exploited as the potential organic substrates in subsurface flow CWs (SSFCWs) with intermittent aeration to investigate the impacts of the varied influent loadings on the removal performance of pollutants. The results indicated that an application of agricultural wastes in CWs presented the different role in improving removal efficiency as influent pollutant loadings increased. In middle and high influent pollutant loadings, CWs with walnut shell strengthened the denitrification process significantly, and could achieve preferable purification of COD (97.36%), NH4+ -N (98.83%), TN (51.78%), and TP (80.33%), respectively. However, N2O emission fluxes were higher in CWs with agricultural biomass and increased clearly as the influent pollutant loadings increasing. The results indicated that combination of agricultural material addition and aeration could be an appropriate intensifying strategy in SSFCWs especially for treating medium-strength low-carbon wastewaters.