As the natural boundary between the Yunnan-Guizhou Plateau and the Hengduan Mountains in China, the large-scale prominent terrain of Ailaoshan Mountain leads to obvious regional differences in climate and vegetation. In this article, a comparative analysis is made on both species composition and floristic components of spore pollen (SP) in two sample soil plots near the main peak of Ailaoshan Mountain. The results show that there is a remarkable difference between the western and eastern sample plots. The climate or meteorology characteristics are likely the main reasons accounting for the differences in habitat characteristics and plant sample investigation results. The tropical genera elements of sediment SPs are higher in the western sample plot (6.8%) than in the eastern sample plot (4.7%) because the western plot is controlled by the Indian summer monsoon at all times. The north temperate elements of sediment SP are lower in the western plot (13.4%) than in the eastern plot (26.4%) because the eastern plot is evidently sometimes influenced by the East Asian winter monsoon. In general, Ailaoshan Mountain may be one of important physical geographical boundaries between the interacting regions influenced by both the Indian summer monsoon and the East Asian winter monsoon.