This study designed two vertical flow constructed wetlands (VFCW) as a secondary treatment for piggery wastewater. The effect of effluent recirculation and substrate type on treatment efficiency of constructed wetlands on piggery waster was firstly investigated. Recirculation considerably improved the removal of NH4-N, total nitrogen (TN), and total phosphorus (TP), but not that of chemical oxygen demand (COD). The natural zeolite-based VFCW performed better than volcanic rock-based VFCW for all four parameters. At the highest recirculation ratio, the average treatment efficiencies of natural zeolite-based VFCW reached 50.7, 91.6, 48.3, and 80.7% for COD, NH4-N, TN, and TP, respectively. The diversity and composition of total bacteria and ammonia-oxidizing bacteria (AOB) in the bioflim of natural zeolite and volcanic rock were then determined. Both total bacteria and AOB in biofilm of natural zeolite were more diverse than those in biofilm of volcanic rock. Phylogenetic analyses further revealed two points: first, genera Alcaligenes and Comamonas dominated in the β-proteobacteria of natural zeolite and volcanic rock, respectively, and second, genera Nitrosospira and Nitrosomonas dominated in AOB of natural zeolite and volcanic rock, respectively. Our results suggest that natural zeolite-based VFCW with effluent recirculation is a good choice for piggery wastewater treatment. In addition, substrate type not only influences nutrients removal, but also plays a part on shaping microbial communities in constructed wetlands.