Chemical properties and molecular diversity of dissolved organic matter (DOM) in agricultural soils are important for soil carbon dynamics and chlorine activity. Yet the chlorine reactivity of soil DOM at the molecular level under agricultural management practices remains unidentified. Here, we investigated the chlorine reactivity of soil DOM under long-term straw return and the molecular activities and transformations during chlorination. The 9-year straw return enhanced the chlorine reactivity of soil DOM, leading to increases in the production of traditional disinfection byproducts (DBPs) and decreases in the formation of emerging high molecular weight DBPs. C17HnOmCl1–2 and C22HnNmOzCl were the highest relative abundances of emerging DBPs. The emerging DBPs were primarily generated through chlorine substitution reactions, with their precursors exhibiting higher H/Cwa (1.47) and O/Cwa (0.41) ratios under straw return. The molecular transformation ability and inactive molecules of soil DOM under long-term straw return were reduced after chlorination, resulting in increased DOM instability. Chlorination led to a shift in the thermodynamic processes of soil DOM molecules from thermodynamically limited to thermodynamically favorable processes, and lignin-like compounds displayed higher potentials for transformation into protein/amino sugar-like compounds. C19H26O6 was identified as a sensitive formula for tracing chlorine reactivity under straw return, and a network illustrating the generation of DBPs from C19H26O6 was established. Overall, these results highlighted the strong chlorine reactivity of soil DOM under long-term straw return.