Soil organic matter (SOM) reserves in paddies are approximately two times larger than those in upland soils, and therefore, rice paddies have a strong impact on terrestrial carbon (C) sequestration. Functional partitioning of SOM into particulate organic matter (POM) and mineral-associated organic matter (MAOM) facilitates our understanding of C sequestration capacity in paddy soils. We analyzed POM and MAOM contents in 104 samples of topsoil and 81 samples of subsoil collected from paddies, and investigated how climate, nitrogen (N) fertilization, and soil depth regulate POM and MAOM storage. MAOM was the predominant fraction (45.3%–63.7%) of SOM in all paddy soils. As the SOC content increased, POM increased linearly, while the increase rate of MAOM slowed down, indicating a tendency for MAOM to reach saturation. The influence of mineral types on POM and MAOM protection exhibited depth-dependent patterns: clay minerals showed stronger associations in topsoil, whereas amorphous iron oxides displayed increasing importance in subsoil. Climatic factors, particularly mean annual temperature (MAT), had contrasting effects on POM and MAOM storage: increasing MAT reduced MAOM content and stability while having a minor impact on POM. Increasing the N application rate had minimal impact on POM and MAOM storage due to crop harvest and the balance between microbial activity and mineral protection mediated by soil acidification. These findings are valuable for facilitating the sequestration and increasing the stability of SOM in paddies, providing information for global soil carbon storage strategies. © 2025 Elsevier B.V., All rights reserved.