The tropical mountainous area of the southeastern Tibetan Plateau (TP) is a hotspot of ecological environment research because of its rich biodiversity. However, limited knowledge regarding modern pollen rain within this area has impeded further investigation of eco-environmental evolution using the pollen record. We collected 62 modern pollen samples from lowland tropics to the subalpine region (740–3550 m a.s.l.) in Medog County, located in the southeastern TP, and performed pollen analysis. Cluster analysis, redundancy analysis, variance partitioning analysis, and boosted regression trees were employed to investigate the relationship between pollen and vegetation/climate. Additionally, Hill numbers (N0, N1, N2) and specificity–occupancy plots were utilized to explore plant diversity. The results indicate that modern pollen rain in Medog reflects well the current characteristics of the vegetation, encompassing both primary and secondary features. Pollen of Cyclobalanopsis, Tsuga and Abies, which are dominant components of the primary vegetation above 2100 m a.s.l., can serve as indicator species for paleovegetation reconstructions. Mean annual precipitation is the most important climatic determinant affecting pollen distribution. Pollen indices reveal that the plant diversity in this study area has a bimodal pattern of ‘relatively high–low–highest–low’ with increasing altitude. The plant diversity above 2100 m a.s.l. is mainly decided by primary vegetation, whereas below 2100 m a.s.l. it can be explained by the intermediate disturbance hypothesis. Furthermore, it is advisable to exercise caution when dealing with arboreal pollen evenness in open mountainous environments due to the increased potential pollen source area caused by valley wind.