•Continuous applications of organic materials increased the C and N fraction content.•Rice straw greatly increased the soil organic C and dissolved organic C content.•Pig manure greatly increased soil microbial biomass N and dissolved total N content. Soil organic carbon (C) and nitrogen (N) pools are the most important soil components, and their characteristics directly or indirectly determine the stability of the soil structure and the soil fertility. Using a rice fields experiment in the coastal areas of Southeast China, how a long-term (10 years) continuous application of organic materials consisting of green manure (Chinese milk vetch), pig manure, and rice straw affected the soil C and N fractions were studied. The results showed that 10-year continuous applications of organic materials to the paddy fields significantly increased the C fraction content in terms of parameters such as the soil organic C (SOC), microbial biomass C (MBC), and active organic C (AOC). It also increased the soil N fraction content, including the soil total N (TN), dissolved total N (DTN), microbial biomass N (MBN), and active N. The rice straw return had the most significant effect in relation to increasing the SOC and dissolved organic C (DOC), with 23.9% and 42.3% increases, respectively, compared to applying chemical fertilizer alone. Organic pig manure had the most significant effect on the soil MBN and DTN, with 49.3% and 50.7% increases, respectively, compared to the application of chemical fertilizer alone. MBC and MBN are the primary components of soil AOC and active N, respectively. The application of organic materials increased the ratio of soil MBC and AOC to SOC, as well as the ratio of MBN, DTN, and active N to the soil TN. Our findings indicated that long-term applications of organic materials could improve and enhance paddy soil fertility and promote increased rice yields.