Rice–crayfish co-culture (RC) has been recognized as a comprehensive ecotype mode. Controversial opinions exist regarding the increase or decrease in global warming potential (GWP) by RC compared with rice monoculture (RM) because N2O and CH4 emission are affected by complex external factors including fertilizer, water management, and temperature (e.g., as in the RC system). However, whether soil from the RC field, except for external conditions, has different characteristics (i.e., organic N and carbon mineralization) that affect N2O and CH4 emission needs clarification. This study aimed to investigate the characteristics of soil organic carbon (SOC) and soil organic nitrogen (SON) mineralization and greenhouse gas emission in soils from RC (RC8 and RC15, indicating 8 and 15 years, respectively) and RM fields using the indoor biological culture method with different water-holding capacity (WHC) levels with a soil moisture content of 30%, 60%, and 90%s. Moreover, the dynamic model of SOC/SON mineralization was fitted to provide data support for fertilization and low-carbon management. RC soil had a higher rate of SOC/SON mineralization that mainly occurred in the first 7 days, and the mineralization rate increased first and then decreased with increasing WHC. The SOC mineralization rate constant (k) showed the trend of RC15 > RC8 > RM at 60% WHC, while the soil from these three fields had similar k values at 30% and 90% WHCs. Further, the half-revolution period of SOC (T1/2) was between 3.395 and 3.665, unlike the k value. The SON mineralization rate constant (k0) showed significant differences, with RC8 > RC15 > RM at 90% WHC, while no significant difference was found at 30% and 60% WHC and the k0 value varied from 0.103 to 0.120 under different WHC levels. RC8 and RC15 soils showed significantly higher soil net ammonification rate (0.5–3.04 g kg− 1 d− 1), net nitrification rate (0.04–0.09 g kg− 1 d− 1), and SON net mineralization rate (0.55–3.13 g kg− 1 d− 1) by more than 67%, 33%, and 65% compared with RM soil. At 30%, 60%, and 90% WHC, cumulative N2O emissions increased by 19–34%, 12–33%, and 17–32% in RC soil than in RM soil, respectively, and RC15 soil showed the highest emission. The cumulative CH4 emission significantly decreased by 23.1% and 11.5% at 30% WHC in RC8 and RC15 soils, respectively, than that of in RM soil. RC soil showed higher soil mineral N content and 31–59% higher GWP compared with those in RM soil, indicating that RC had higher mineral N support, while also having higher carbon emission risk. Therefore, N fertilizer can be reduced to a certain extent for long-time RC fields, and other effective low-carbon measures (e.g., enhanced-efficiency fertilizer, deep fertilization, and straw management) can be adopted to reduce GWP.