The research provides new insights into how T. tubifex affects microbe-available organic carbon transformation, microbial community, and related inorganic nitrogen transformation. With different T. tubifex densities under enriched NO3-N concentration with different C/N ratio, the groups with low and high T. tubifex abundance had 17.1% and 27.2% higher TOC concentrations compared to control group under C/N ratio of 3.0 and 2.0, respectively. According to the OC characteristics analyzed by GC–MS and EEM, the group with T. tubifex contained higher dissolved organic carbon (DOC) content and short-chain compounds. As the NO3-N concentration increased and C/N ratio decreased, the proportions of carboxylic acid derivatives (methyl acetate), sulfur-containing compounds, humic-like products and the emission of CO2 were enhanced with T. tubifex, which could be utilized by denitrifiers directly. The OC degradation was highly correlated with the effect of T. tubifex on microbial community and nutrient removal. The T. tubifex can increase OC transformed into sediment and change the microbial community similarity to that in their digestive system. According to the principal component analysis (PCA), the improved proportions of OC that available for microbes and altered microbial community with T. tubifex could enhance denitrification, which experienced a 21% higher denitrifiers and threefold increased NO3-N removal efficiency than that in control group.