Palynological analysis was carried out on 81 samples of topsoils and mosses collected from four different landforms in the karst areas of Chongqing City, Southwestern China. The results are summarized here. (1) A total of 109 pollen taxa (genera or family) were identified, which were dominated by herbs and ferns, followed by trees (mainly Pinus massoniana); shrub pollen content was the lowest (excluding Mt. Jinfo). These results revealed serious degradation of vegetation in the study area. (2) PCA analysis could distinguish the modern samples, which better reflects the characteristics of pollen assemblages in the karst areas, especially in the rocky desertification areas. In Mt. Jinfo with good ecological protection and natural vegetation development, we found 106 families of trees, shrubs and herbaceous pollen types, and a high content of arboreal pollen. On the contrary, fewer types of trees and shrubs were found in the karst rocky desertification areas, such as Mt. Jigong (46 families), Qingmuguan Town (56 families), and Nanping Town (50 families). (3) As the unique relict plant of Mt. Jinfo, the percentage of Cathaya argyrophylla pollen was much lower than that of Pinus pollen, indicating that its pollen is not suitable for long-distance transmission. (4) The proportions of trees and shrubs pollen decreased with the increasing land use intensity, while those of herbs and ferns increased, which were heavily dominated by pollen of weeds. Therefore, we conclude that the change in land use is the main factor affecting the secondary vegetation and pollen assemblages in the karst areas we studied. The results can provide some guidance for land use decision-making for the Chongqing karst areas, and can also provide some basic data and reference for Quaternary paleo-vegetation, paleoclimate and paleoenvironment reconstructions in Chongqing and its surrounding areas, and for the construction of the China Pollen Database.