There is limited knowledge regarding the differences and relationships in molecular composition between dissolved organic matters (DOM) and dissolved organic nitrogen (DON) in autotrophic and heterotrophic nitrogen removal processes. In this study, the composition of DOM and DON during two full-scale wastewater treatment plants (WWTPs), an autotrophic nitrogen removal with partial nitrification-anammox process (PN/A) and a heterotrophic nitrogen removal with anaerobic/anoxic/oxic process (A2O), were systematically investigated by using ultraviolet–visible spectroscopy, Excitation-Emission Matrix (EEM) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The results indicated that both PN/A and A2O resulted a decrease in molecular diversity and bio-availability of DOM. However, there were distinct variations in DON between the two processes. In PN/A, transformation of DOM and DON was found to be coupled, while there was a lack of correlation observed between DOM and DON in A2O. Pearson correlation analysis revealed that transformation of DOM and DON in WWTPs was associated with microbial roles. During biotreatment, PN/A exhibited a higher metabolic capacity for degrading high bio-available and high aromatic compounds compared to A2O. The autotrophic nitrogen removal unit in PN/A resulted in an increase in molecular weight (MW) of DON, as well as a decrease in bio-availability and unsaturation degree of DON. Therefore, autotrophic nitrogen removal unit may have a positive influence on control of eutrophication and disinfection by-products (DBPs) formation. This study improved the understanding of molecular composition and relationship between DOM and DON, as well as microbial roles on DON transformation within autotrophic and heterotrophic nitrogen removal processes.