Methanogenesis and syntrophy are the most important microbial metabolic processes for the anaerobic decomposition of organic matters in paddy soils. However, the diversity and abundance of syntrophic communities and their ecological determinants remain largely unexplored. In this study, we aimed to unravel the impacts of soil type and rice phenology on both syntrophic and methanogenic communities. The relative abundances of syntrophic bacteria and methanogenic archaea were significantly affected by soil type and rice growth stages, with 0.39–1.66% and 1.68–3.95% for syntrophic bacteria and 0.49–6.04% and 9.29–13.69% for methanogenic archaea, respectively. Besides, the populations of short-chain fatty acid-degrading syntrophs (SFAS) varied across soil types (range: 8.21 × 106–7.83 × 107 16S rRNA gene copies g−1 dry soil) and rice growth stages (range: 2.27 × 107–3.88 × 107 16S rRNA gene copies g−1 dry soil). Moreover, the populations of syntrophic propionate-oxidizing bacteria were 1.2–6.2 times higher than those of butyrate-oxidizing bacteria in the 10 paddy soils during the off-rice season, indicating that propionate is the main intermediate product during anaerobic decomposition of organic matter. However, Syntrophomonas was the most dominant throughout the rice growing season, implying that syntrophic pathways may vary between off-rice and growing seasons. Interestingly, the populations of SFAS and methanogens showed a significantly positive correlation (P < 0.05). This suggests that syntrophic bacteria, in cooperation with methanogenic archaea, can affect methane production in paddy soils. Furthermore, C/N ratio, soil moisture, soil pH, oxalate, citrate, and their interaction accounted for 65.20% of the changes in syntrophic communities. Altogether, our findings indicate that soil type, rice phenological stages and soil properties can shape the distribution of syntrophic communities in rice paddy fields.