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.　©　2023　Elsevier　B.V.