To understand the role of paddy soils in the global carbon cycle, it is necessary to analyze the characteristics of the organic carbon pool at different soil depths. It was hypothesized that soil organic carbon fractions including labile organic carbon fraction I (LOCF-I), labile organic carbon fraction II (LOCF-II), and recalcitrant organic carbon (ROC) distributed differently within the soil profile. In this study, soil was collected from 27 typical rice fields in Guangdong Province, south China. The carbon fractions of the paddy field soils were analyzed and compared over a 0–60 cm depth profile. The relationship between carbon content and the physical and chemical properties of the soils was further analyzed using correlation analysis and structural equation modeling. The results showed that soil total organic carbon concentration in paddy fields was increased by 22.1% during the last four decades. In the soil organic carbon pool of 0–60 cm profile, the proportion of 67.31 to 70.31% in ROC, 21.75 to 22.06% in LOCF-I, and 7.7 to 10.63% was recorded, respectively, indicating that ROC was the dominating fraction. Storage of soil total organic carbon and fractions all decreased with the increase in soil depth. Correlation and path analysis showed that total nitrogen was the main driving factor affecting the soil carbon fractions, whereas pH and soil bulk density indirectly affected the content of carbon fractions by influencing total nitrogen. The results imply the importance of soil total nitrogen in paddy carbon management of rice cultivation.