Display omitted •Faster NOM reaction with •OH than SO4•− was examined using FTICR MS.•NOM reactivity towards SO4•− was highly electron density-dependent.•Reactivity to •OH was co-shaped by aromaticity, molecular size and composition.•SO4•− reaction occurred slower through electron transfer and decarboxylation.••OH reacted faster through radical addition and H-abstraction. The higher scavenging capacity of natural organic matter (NOM) to hydroxyl radical (•OH) than sulfate radical (SO4•−) has been long-acknowledged. However, the difference in reactivity and the influence of initial characteristics, especially at the molecular-level, remain unaddressed. In this study, the reactivities of different NOM isolates to •OH and SO4•− were compared based on the determined second-order rate constants following the depletion of UV254-absorbing moieties. Three NOM isolates with varying characteristics were selected to investigate the influence of initial characteristics on their reactivities. With the identified reactive molecules using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), the distinct reactivity between the radicals and the influence of the initial characteristics were illustrated. The reactivity towards SO4•− was dominated by the electron density of the molecules (i.e., double bond equivalent (DBE)), while that of •OH was also shaped by molecular size (i.e., m/z) and composition (i.e., N- or S-incorporation). The examination on the exclusively reactive molecules (accounting for 10–20%) reflected a preferred H-abstraction by •OH and decarboxylation by SO4•−. Moreover, the analysis on the shared reactive molecules (80–90%) based on the UV254 versus electron-donating capacity (EDC) dependency revealed a prevalent •OH addition while single electron transfer to SO4•−. The different reaction rates associated with the proposed transformation pathways supported the observed higher reactivity of NOM to •OH than SO4•−.