Karst rocky desertification, a kind of intense soil degradation, has become an urgent environmental issue in the karst region of southwest China. It was found that limestone soil, a typical soil of the karst region, is more vulnerable to karst rocky desertification than adjacent other soils although limestone soil has relatively high TOC (total organic carbon) content, but underlying mechanisms remain unclear. To investigate roles of soil properties in karst rocky desertification, three major soils, limestone soil, yellow soil and yellow brown soil, of the karst region of southwest China were sampled and their total extractable humic acid (THA) were fractionated into three sub-fractions, namely, free HA (HAf), encapsulated HA (HAe) and interacted HA (HAi), with a sequential extraction method. These soils and fractionated HA samples were systematically characterized with various analysis methods and discussed. The results showed that limestone soil had higher contents of total organic content (TOC) and THA content, but its THAC/TOC (carbon in THA to TOC) ratio (23.39%) was lower than those of yellow soil (31.44%) and yellow-brown soil (30.74%); C/N ratios and total acid contents of HAe and HAi fractions, which were physically protected by soil minerals/aggregates, were much higher than those of HAf fractions, indicating that HAe and HAi could be more active and degraded easier than HAf once exposed to microbes or/and runoff erosions. Therefore, lower HAf content and significantly lower HAfC/TOC (carbon in HAf to TOC) ratio of limestone soil may underlie the observation that limestone soil showed weak resistance to karst rocky desertification compared to other adjacent soils when the site had been artificial disturbed. We believe that roles of different HA fractions to overall quality and stability of soil deserve more attention.