Biological treatment processes perform satisfactory in wastewater treatment, but the relatively high cost and complicated maintenance limit its application in rural areas. In this study, a highly packed biofilm reactor (HPBR), with a 90% packing ratio of carriers in the bioreactor, was designed for rural wastewater treatment. The results showed that the removal rates for chemical oxygen demand (COD) and ammonia were 3.04 ± 1.81 kg/m3/d and 0.49 ± 0.18 kg/m3/d, respectively. Besides, the removal efficiency of total inorganic nitrogen (TIN) was 35.4% by the HPBR. The removal capacity of the HPBR is higher than other reported systems with fewer operational costs and maintenance. High-throughput sequencing was applied to further investigate the kinetics and principals. Microorganisms capable of simultaneous nitrification-denitrification were found to be dominant species in the HPBR system, which indicated that the nitrogen removal in HPBR is governed by simultaneous nitrification-denitrification. These findings suggest that HPBR can be used as an efficient reactor for rural wastewater treatment, demonstrating its feasibility in real applications.