Removal of nitrogen from wastewater with low carbon/nitrogen ratio was treated by using a denitrification packed bed reactor. Composite fillers with both autotrophic and heterotrophic denitrification capacity were prepared by mixing melted polycaprolactone and elemental sulfur at various alkalinity ratios (heterotrophic to autotrophic ratios of 1:2, 1:1, 3:2, and 2:1). Optimum denitrification was achieved at a ratio of 2:1. The diversity of the microbial community in the biofilm on the surface of the composite fillers showed that the increase of the elemental sulfur in the composite fillers has led to the increase of the microbial abundance. Furthermore, biofilm composition developed from a single dominant species to multiple species, and genes related to sulfur metabolism increased while those related to denitrification decreased slightly. Display omitted •New composite fillers with mixotrophic denitrification capacity were synthesized.•The pH of the system was well balanced with the filler prepared 2:1 alkalinity ratio.•No accumulation of NO2−-N was observed with NO3− of 30 mg/L in the influent.•Genes related to sulfur metabolism is increased in the mixotrophic system.