Owing to intensive cultivation, paddy fields suffer from varying degrees of degradation and loss of soil organic carbon (SOC), consequently jeopardizing the industry’s future sustainability. Accurate assessment of soil nutrient loss and SOC stability is not only indispensable for developing measures to arrest and counter this problem but to also gauge the impact of degraded soils in paddy fields towards the global carbon budget. Herein, we examine soil nutrients, their stoichiometric ratios, and carbon pool management index (CPMI) across 26 paddy fields in a subtropical region under three degraded levels – namely, low-risk degradation, high-risk degradation, and severe degradation. Our results showed a 23% likelihood of severe degradation in sampled paddy fields of southeastern China. Compared with low-risk degradation soils, the severe degradation soils had significantly lower concentrations of total nitrogen (N) (31%), labile organic carbon (C) (50%), total phosphorus (P), and available P concentrations, while the iron (Fe) and available N tended to increase. Compared to low-risk degradation, C:N, C:P, N:P ratios were 25, 50, and 30%, respectively, lower in severe degradation plots. Low CPMI values were associated with soils that are at high-risk for degradation and severe degradation, indicating that C pools in degraded paddy soils were gradually deteriorating. Moreover, soil stoichiometric ratio and nutrients were significantly affected by soil pH, Fe³⁺, sand, and electrical conductivity, and there were significant and positive correlations between CPMI and soil C, N and LOC concentrations. Based on the above results, our work provided evidence that paddy degradation led to a greater loss of soil carbon and nitrogen than phosphorus, reducing the soil’s potential for C sequestration. Therefore, adopting proper agricultural practices whilst minimizing the cultivation of exhaustive crops could mitigate further soil degradation and assist in restoring soil fertility and C sequestration in paddy fields of Southeastern China.