The pollen analysis of 25 topsoil and mosses samples under six typical types of vegetations in the Karst rocky desertification area showed that: 1) 47 pollen taxes are recorded totally, among which, herbs and ferns are dominate with 23.62%~76.47%, then the trees (mainly Pinus massoniana) with 17.73%~74.05%, and the shrub pollen is only about 0~12.50%, indicating the character of a serious degradation of local vegetation; and 2) pollen assemblages are obvious differentiation under different vegetations, which corresponding to the actual vegetation and reflecting the present conditions of the modern vegetation in the rocky desertification area, indicating pollen analysis can give a reference to the rehabilitation and reconstruction of natural environment in the study area.