Comprehensive understanding of the modern pollen–vegetation relationship is crucial for utilizing fossil pollen to reconstruct palaeovegetation, especially in mountainous areas of southwestern China. In this study, we present forty-five modern surface samples collected from five different vegetation communities of the southern Gaoligong Mountains region, and the vegetation composition was investigated at each sample site. The modern pollen assemblages were analyzed through multivariate analysis to evaluate the relationships between vegetation types and pollen assemblages, and to investigate the representation of major pollen types in different vegetation types. The results indicate that the surface pollen assemblages of different vegetation types reliably represent the modern vegetation. The median R-values of dominant pollen taxa in the Gaoligong Mountains region can be ordered as follows: Pinus > Alnus > Poaceae > evergreen Quercus. The over-representation of Pinus pollen, attributed to its high productivity and strong dispersal ability, makes it the dominant component of exotic pollen. Conversely, the under-representation of evergreen Quercus suggests that the presence of its pollen within a sample might indicate the growth of the local parent plant in the study area. The human activities in the region have a recognizable effect on the surface pollen spectra and also exert a significant negative impact on pollen diversity. Our study supplements the modern pollen database of the mountain regions in southwestern China, and provides representative modern pollen analogues to interpret fossil pollen records from southwestern China and similar regions.