With global eutrophication and increasingly stringent nitrogen discharge restrictions, dissolved organic nitrogen (DON) holds considerable potential to upgrade advanced wastewater denitrification because of its large contribution to low-nitrogen effluents and stronger stimulation effect for algae. Here, we show that DON from the postdenitrification systems dominates effluent eutrophication potential under different carbon sources. Methanol resulted in significantly lower DON concentrations (0.84 ± 0.03 mg/L) compared with the total nitrogen removal-preferred acetate (1.11 ± 0.02 mg/L) (p < 0.05, ANOVA). With our well-developed mathematical model (R2 = 0.867-0.958), produced DON instead of shared (persist in both influent and effluent) and/or removed DON was identified as the key component for effluent DON variation (Pearson r = 0.992, p < 0.01). The partial least-squares path modeling analysis showed that it is the microbial community (r = 0.947, p < 0.01) rather than the predicted metabolic functions (r = 0.040, p > 0.1) that affected produced DON. Carbon sources rebuild the microorganism-DON interaction by affecting the structure of microbial communities with different abilities to generate and recapture produced DON to finally regulate effluent DON. This study revalues the importance of carbon source selection and overturns the current rationality of pursuing only the total nitrogen removal efficiency by emphasizing DON.