[Objective] The mechanism and effects of red soil degradation were elucidated in order to provide scientific basis to soil and water conservation and rocky desertification effect of the east Yunnan Platean. [Methods] This study examined the mountainous red soil based on the analysis of soil profile aggregates associated with different vegetation types, as well as the distribution of organic matter. Particularly, soil samples were taken from area covered with pine, shrubland, grassland or unvegetated red soils respectively in the karst area of east Yunnan Province. [Results] The degraded soils were characterized by large aggregates after dry sieving, the contents of which generally decreased with depth. The highest content was micro-aggregates after wet sieving and samples from vegetation-covered area showed a similar trend as that with dry sieving, while the red bare soil showed the a trend of 0-90 cm (B layer) > 90-100 cm (C layer). Degree of stability and content of organic matter displayed a trend of shrub lands > pineland > grassland > red bare soil during the degradation process. Soil aggregate stability and physical properties of soils from shrubland, pineland and grassland gradually decreased and soil organic matter(SOM) deteriorated with increase of depth. On the contrary, all the proxies of red bare soil showed an opposite trend. In contrast to A and B layers, the structural property became inferior, and the content of SOM of C layer decreased significantly. [Conclusion] There was a significant and positive correlation between the content of SOM and mean weight diameter, geometric mean diameter and >2 mm size aggregate content, but a significant negative correlation between SOM and fractal dimension. All these suggest the possible and viable way to improve the structural condition of red bare soil by increasing the content of SOM.