A long-term field experiment was conducted since 1981 in order to explore the effects of underground water table and organic manure on labile carbon fractions (light fraction organic carbon, LFOC; easily oxidized carbon, EOC; and particulate organic carbon, POC) as well as the interaction relation of aggregates and porosity on labile carbon fractions, the treatments included two underground water tables of 20 cm and 80 cm, applying organic manure with a high rate (HOM) and a normal rate (NOM), and applying chemical fertilizer (CF). The results showed that lowering underground water table resulted in significant lower content of LFOC and POC under NOM and CF, and the contents of EOC were increased significantly under different treatments; long-term application of organic manure significantly increased the contents of LFOC, EOC and POC. Two-way ANOVA revealed that the fertilization had a greater effect on labile carbon fractions than underground water table. The increased content of macro aggregates in red paddy soil could promote the formation of capillary pores, which protected or stabilized LFOC and POC; however, no obvious effect of porosity and aggregates on EOC was observed. Therefore, it is necessary to pay attention to the change of groundwater level and the rational application of organic manure in soil organic carbon management and fertility regulation of paddy fields in south China.