Paddy soils make up the largest anthropogenic wetlands on earth, and are characterized by a prominent potential for organic carbon (C) sequestration. By quantifying the plant‐ and microbial‐derived C in soils across four climate zones, we identified that organic C accrual is achieved via contrasting pathways in paddy and upland soils. Paddies are 39%–127% more efficient in soil organic C (SOC) sequestration than their adjacent upland counterparts, with greater differences in warmer than cooler climates. Upland soils are more replenished by microbial‐derived C, whereas paddy soils are enriched with a greater proportion of plant‐derived C, because of the retarded microbial decomposition under anaerobic conditions induced by the flooding of paddies. Under both land‐use types, the maximal contribution of plant residues to SOC is at intermediate mean annual temperature (15–20°C), neutral soil (pH~7.3), and low clay/sand ratio. By contrast, high temperature (~24°C), low soil pH (~5), and large clay/sand ratio are favorable for strengthening the contribution of microbial necromass. The greater contribution of microbial necromass to SOC in waterlogged paddies in warmer climates is likely due to the fast anabolism from bacteria, whereas fungi are unlikely to be involved as they are aerobic. In the scenario of land‐use conversion from paddy to upland, a total of 504 Tg C may be lost as CO₂ from paddy soils (0–15 cm) solely in eastern China, with 90% released from the less protected plant‐derived C. Hence, preserving paddy systems and other anthropogenic wetlands and increasing their C storage through sustainable management are critical for maintaining global soil C stock and mitigating climate change.

Incorporation of crop residues is essential to enhance soil organic matter in arable ecosystems. Here, we monitored the dynamics of cellulose and lignin, the most abundant constituents of plant residues, and their relationships with enzyme activities, microbial gene abundances and soil properties after 13-year long-term and one-year short-term crop straw incorporation into upland and upland-paddy soils in a field-based experiment. Lignin, rather than cellulose, accumulated in both soils following straw incorporation. Cellulose was almost completely converted into non-cellulose forms within 6 and 3 months after straw incorporation into upland and upland-paddy rotation soils, respectively. Whereas, lignin accumulated at the rate of 129 and 137 mg kg⁻¹yr⁻¹within 13 years’ straw incorporation in upland and upland-paddy rotation, respectively. The predominance of recalcitrant vanillyl monomers in upland-paddy rotation indicated a high stability of lignin. Structural equation models revealed that the key factor driving cellulose and lignin dynamics was available nitrogen, followed by enzymes activities (cellobiohydrolases and laccases) and functional genes abundances (cbhI andlaccase-like) as mediated by soil pH. Our findings highlighted that upland might have higher carbon sequestration rate, whereas upland-paddy rotation system was more beneficial for accumulation of recalcitrant organic fractions under crop residue incorporation.