To study the efficiency and mechanism of nitrogen and phosphorus removal for decentralized rural sewage in modified zeolite wetland, the modified zeolite was applied as substrate into a combined process composed of anaerobic baffled reactor (ABR) and baffled flow constructed wetland (BFCW), providing a new way for rural sewage treatment in Suzhou City. The study was contrasted with zeolite wetland. The results showed that the modified zeolite wetland had high efficiency and stability of nitrogen and phosphorus removal, and the nitrogen and phosphorus removal quantities of modified zeolite wetland were 1.8% and 1 times higher than those of zeolite wetland during the trial. The modified zeolite wetland mainly removed nitrogen and phosphorus by substrate adsorption, and the main fractions of modified zeolite were Ca-P and Al-P. The oxygen-secretion and absorption of plants stabilized the water quality of the effluent. The substrate adsorption was the main nitrification removal pathway in front of the wetland, and nitrification and denitrification were the main nitrification removal pathways at the end of the wetland. The nitrogen and phosphorus adsorption capacities during the pilot test were much higher than those of the static test. The optimization of phosphorus adsorption capacity for modified zeolite was achieved under the synergy of multiple pathways. The effect of configuration and plant root was the main reason for the difference of nitrogen and phosphorus adsorption quantities. Nitrification intensity led to the seasonal fluctuation of nitrogen removal effect and stability in modified zeolite wetland, and the low nitrification intensity in the front of wetland was related to the strong adsorption of NH4+-N by the modified zeolite.