A pilot scale experiment was conducted to evaluate the characteristics of contaminants removal in a continuously two-stage biological process composed of an anoxic biofilter (AF) and an biological aerated filter (BAF). This novel process was developed by introducing new composite packing material (MZF) into bioreactors to treat rural domestic wastewater. A comparative study conducted by the same process with ceramsite as packing material under the same conditions showed that a MZF system with a Fe proportion in the packing material performed better in chemical oxygen demand (COD) removal (average 91.5%), ammonia (NH4+-N) removal (average 98.3%), total nitrogen (TN) removal (average 64.8%) and total phosphorus (TP) removal (average 90%). After treatment of the MZF system, the concentrations of COD, NH4+-N, TN and TP in effluent were 20.3 mg/L, 0.5 mg/L, 11.5 mg/L and 0.3 mg/L, respectively. The simultaneously high efficiencies of nitrification, denitrification and phosphorus removal were achieved by the coupling effects of biological and chemical processes in the MZF system. The results of this study showed that the application of MZF might be a favorable choice as packing material in biofilters for treatment of rural domestic wastewater.