Background and aims: Dissolved organic matter (DOM) is an active component of the soil organic carbon (SOC) and nitrogen (N) pool. However, the relationship between DOM chemodiversity and microbial communities, and their effects on the C and N in paddy fields under organic or inorganic fertilization, are poorly understood but important for sustainable agricultural production. Methods: We conducted a six-year experiment in paddy fields under the following different organic and inorganic fertilizer treatments: no fertilizer (CK), chemical fertilizer (150 kg·hm−2 N; CF), 50% N from chemical fertilizer + 50% N from decomposed cattle manure (CMF50), and manure fertilizer (100% N from decomposed cattle manure; MF). Results: CMF50 exhibited the highest yield (10.89% increase compared with CF). MF and CMF50 enriched the availability and content of soil N, which in turn exhibited a strong effect on net N mineralization and increased SOC and the amount of recalcitrant components of DOM. However, the continuous use of CF led to an increase in both soil bulk density and the number of anaerobic organisms Anaerolinea and Bellilinea. The fractions of DOM containing lignin-like and lipid-like compounds were strongly correlated with Anaerolinea and Bellilinea and contributed to net N mineralization and SOC. Continuous use of CF facilitated net N mineralization but decreased both DOC and SOC. Conclusions: Continuous applications of CMF50 and MF improved the microbial communities and increased the recalcitrant components of DOM, thus highlighting the importance of the relationship between DOM composition and soil microbial communities while assessing the soil N and SOC. [ABSTRACT FROM AUTHOR]