Soil-derived dissolved organic matter (SDOM) is an important site-specific disinfection byproduct (DBP) precursor in watersheds. However, it remains unclear how fertilization regime shifts the molecular diversity and chlorine reactivity of SDOM in cropland-impacted watersheds. Here, we analyzed the spectroscopic and molecular-level characteristics of the SDOM from croplands that had different fertilization regimes (i.e., non-fertilization, chemical fertilization, straw return, and chemical fertilization plus straw return) for 5 years and evaluated the chlorine reactivity of the SDOM by determining the 24-h chlorine consumption and specific DBP formation potential (SDBP-FP). The SDOM level decreased by chemical fertilization and was not significantly altered by straw return alone or combined with chemical fertilizer. However, all fertilization regimes elevated the molecular diversity of SDOM by increasing the abundance of protein-, lignin-, and tannin-like compounds. The chlorine reactivity of SDOM was reduced by chemical fertilization, but was significantly increased by straw return. Typically, straw return increased the formation potential of specific trihalomethane and chloral hydrate by 339% and 56% via increasing the aromatics in SDOM, whereas chemical fertilization could effectively decrease about 231% of the increased specific trihalomethane formation potential caused by straw return. This study highlights that fertilization regime can significantly shape the molecular diversity and chlorine reactivity of the SDOM in croplands and that partially replacing chemical fertilizer with crop straw is an advantageous practice for reducing DBP risks in drinking water in cropland-impacted watersheds.