Soil organic matter (SOM), along with the rock weathering, originating from the residues of animals, plants and microorganisms involved in soil formation and evolution. The stability of SOM could directly produce an effect on carbon sequestration. To elucidate the stability characteristics of SOM in karst areas at the molecular structure level, in this study, the humic acids (HA), as the major proxy of SOM, were extracted, purified, and ultra-filtrated. The HA from calcareous soil were fractionated into five size fractions, while the HA from yellow soil were separated into eight size fractions. Via the analysis of potentiometric titration, FTIR, and CPMAS C-13 NMR, the results showed some common features, whereby compared with the bigger size fractions, the smaller size fractions have much lower contents of aliphatic carbon, but have higher contents of aromatic carbon, carboxyl groups, ketonic groups, phenolic hydroxyl groups, and total acidity, which indicates that the smaller size fractions are more soluble as well as more degradable than the bigger ones. It was distinct that, in the size fractions of HA from calcareous soil, negative correlations between the acidic functional groups' contents and the oxygen contents were found, suggesting that the oxygen was mainly located in the hydroxyl group of carbohydrates instead of carboxyl and hydroxyl groups in aromatic rings, and confirming that the bigger size fractions have much higher contents of carbohydrate subunits. According to the analysis, comparing with the HA in yellow soil, we presumed that the HA from calcareous soil were more polar and degradable. However HA from calcareous soil had a larger molecular size than that of HA from yellow soil, as well as, calcareous soil had a higher content of SOM than that of the same layer of yellow soil which suggests that the conservation mechanism of HA in calcareous is not only the organic molecular structure resistance but also the chemical protection from forming complexes with calcium or/and physical protection from enclosing by hypergene CaCO3 precipitation.