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Long-term application of soil organic amendments (SOA) can improve the formation of soil organic carbon (SOC) pool as well as soil fertility and health of paddy lands. However, the effects of SOA may vary with the input amount and its characteristics. In this work, a descriptive field research was conducted during one cropping season to investigate the responses of various SOC fractions to different long-term fertilization practices in rice fields and their relationships with soil biogeochemical properties and the emission of greenhouse gases (GHG). The field sites included two conventional paddies applied with chemical fertilizer (CF) or CF + rice straw (RS) and six organic agriculture paddies applied with oilseed cake manure (OCM) + wheat straw (WS), cow manure (CM) + WS, or CM + RS. The two paddy soils treated with CM + RS had significantly higher concentrations of recalcitrant to labile C forms, such as loss-on-ignition C (LOIC; 56–73 g kg−1), Walkley–Black C (WBC; 20–25 g kg−1), permanganate oxidizable C (POXC; 835–853 mg kg−1), and microbial biomass carbon (MBC; 133–141 mg kg−1), than soils treated with other SOA. Likewise, long-term application of CM + RS seemed to be the best for regulating soil fertility parameters, such as ammonium (11–141 mg kg−1); phosphate (61–106 mg kg−1); and soluble Ca, K, and Mg (7–10, 0.5–1.2, and 1.9–3.8 mg kg−1, respectively), although the results varied with the location and soil properties of rice fields. Additionally, the two paddy sites had the largest cumulative methane emission (754–762 kg ha−1), seemingly attributed to increased microbial biomass and labile C fractions. The significant correlations of most SOC fractions with soil microbial biomass, trophic factors, and methane emissions were confirmed with multivariate data analysis. It was also possible to infer that long-term SOA application, especially with CM + RS, enhanced interaction in belowground paddy fields, contributing to soil fertility and rice production sustainability. Based on our findings, we suggest the need for analysis of various types of SOC fractions to efficiently manage soil fertility and quality of paddy fields, C sequestration, and GHG emissions. [ABSTRACT FROM AUTHOR]