Fertilizer management has the potential to promote the storage of carbon and nitrogen in agricultural soils and thus may contribute to crop sustainability and mitigation of global warming. In this study, the effects of fertilizer practices [no fertilizer (Control), chemical fertilizer (NPK), Compost, and chemical fertilizer plus compost] on soil total carbon (TC) and total nitrogen (TN) contents in inner soil profiles of paddy soil at 0-60 cm depth were examined by using long-term field experimental site at $42^{nd}$ years after installation. TC and TN concentrations of the treatments which included N input (NPK, Compost, NPK+Compost) in plow layer (0-15 cm) ranged from 19.0 to 26.4 g $kg^{-1}$ and 2.15 to 2.53 g $kg^{-1}$, respectively. Compared with control treatment, SOC (soil organic C) and TN concentrations were increased by 24.1 and 31.0%, 57.6 and 49.7%, and 72.2 and 54.5% for NPK, Compost, and NPK+Compost, respectively. However, long term fertilization significantly influenced TC concentration and pools to 30 cm depth. TC and TN pools for NPK, Compost, NPK+Compost in 0-30 cm depth ranged from 44.8 to 56.8 Mg $ha^{-1}$ and 5.78 to 6.49 Mg $ha^{-1}$, respectively. TC and TN pools were greater by 10.5 and 21.4%, 30.3 and 29.6%, and 39.9 and 36.3% in N input treatments (NPK, Compost, NPK+Compost) than in control treatment. These resulted from the formation and stability of aggregate in paddy soil with continuous mono rice cultivation. Therefore, fertilization practice could contribute to the storage of C and N in paddy soil, especially, organic amendments with chemical fertilizers may be alternative practices to sequester carbon and nitrogen in agricultural soil.