Dissolved organic matter (DOM) plays a critical role in soil biogeochemical processes and affects the responses of soil organic matter (SOM) to agricultural practices. However, the effect of converting forests to intensive orchards on the chemodiversity of soil DOM remains poorly understood. In this study, we systematically investigated molecular-scale transformations in soil DOM resulting from the conversion of Chinese fir ( Cunninghamia lanceolata [Lamb.] Hook) plantations to citrus orchards of varying ages (10, 30, and 50 years) using an integrative approach combining UV–Vis spectroscopy, EEM–PARAFAC, and FT-ICR MS. Long-term citrus cultivation promoted the stabilization of DOM, which was associated with increased aromaticity (SUVA 524, SUVA 280), oxidation (O/C wa: 0.440 to 0.566), and molecular weight (m/z wa: 395.977 to 413.460), alongside decreased aliphaticity (H/C wa: 1.368 to 1.023). In 50-year orchards, recalcitrant compounds dominated the DOM pool (87.7% vs. an initial 77.9%), and the abundance of combustion-derived polycyclic aromatics (+1,292%) and lignin derivatives (from 2,204 to 4,485 molecules) increased. In contrast, microbial-derived components (e.g., proteins and carbohydrates) declined substantially with prolonged cultivation. Soil acidification (pH 5.42 to 4.08) and organic fertilization jointly enhanced the formation of aromatic-condensed DOM structures, with the 30-year stage marking a critical transition in humification processes. These findings underscore the role of agricultural intensification in shaping soil carbon persistence and provide molecular-level insights to inform carbon sequestration strategies in managed ecosystems.