Abstract: Soil iron oxide indicates soil-forming process and soil-forming environment under which the iron oxide was formed. Soil iron oxides of natural soils and agriculture soils in different phases of Karst rocky desertification in southwestern China were analyzed this time. The distributions of soil total iron (Fet), free iron oxide (Fed) and amorphous iron (Feo) were also studied, and soil-forming process in the Karst rocky desertification regions was discussed. The results were as follows: the soil total iron content in Karst region ranges from 38.9~53.9 g/kg. The free iron oxide content ranges from 18.0~26.7 g/kg. The degree of free iron ranges from 44.1% to 73.4%, and the degree of active iron ranges from 7.2% to 11.4%. With the aggravation of rocky desertification, the free iron oxide content and the free iron degree increase, and the degree of active iron decreases. The degree of free iron and the active iron of different profile in karst natural soils in surface layer is larger than bottom layer, but the degree of free iron in agriculture soil in bottom layer is larger than surface layer. The soil-forming process of karst region is due to limestone corrosion. Under anthropogenic disturbance, the essence of rocky desertification process in natural soils is soil and water erosion process in surface layer, and that in agriculture soils was "soil loss" process which was affected by water vertical migration.