The effects of diatomite on the distribution, stability, and carbon and nitrogen content of soil aggregates in paddy fields were investigated to provide a theoretical foundation for optimizing fertilization practices and improving carbon and nitrogen sequestration. A field experiment was conducted in 2021 in Jingzhou City, Hubei Province, to analyze the impacts of four fertilization treatments: no application of diatomite or nitrogen fertilizer (CK), conventional chemical fertilizer (NPK), diatomite application alone (Si), and the combined application of chemical fertilizer and diatomite (NPKSi) on the composition of soil aggregates and the distribution of carbon and nitrogen within the 0–20 cm tillage layer. Results indicated that, compared with CK, NPK and NPKSi treatments significantly increased the proportion of >0.25 mm aggregates by 2.66% and 8.28%, respectively, while reducing the proportion of silt and clay particles (<0.053 mm aggregates) by 14.99% and 22.50%, respectively. The mean weight diameter (MWD) and geometric mean diameter (GMD) followed the order: Si < CK < NPK < NPKSi. NPK and NPKSi treatments significantly enhanced soil organic carbon (SOC) content and stock, with increases of 10.60% and 17.67%, and 8.84% and 14.42%, respectively, compared to CK, whereas the Si treatment showed no significant difference. Additionally, the NPKSi treatment markedly improved soil total nitrogen (TN) content and stock, outperforming all other treatments. Across different aggregate sizes, NPK and NPKSi treatments increased organic carbon and total nitrogen content, whereas the Si treatment caused a slight decrease. Super aggregates (>2 mm) under NPK and NPKSi treatments contributed the most to organic carbon and total nitrogen, with contribution rates of 30.91% and 36.71%, and 32.81% and 38.99%, respectively. In conclusion, the combined application of diatomite and nitrogen fertilizer significantly increased the proportion of large aggregates, improved aggregate stability, and enhanced the contribution rates of organic carbon and total nitrogen, thereby effectively boosting carbon and nitrogen storage in paddy soils.