Previous studies of pollen in northern Borneo lack basic data on surface soil pollen as a basis for the quantitative reconstruction of paleoclimate and modern palynological comparison. In this study, we conducted palynological analysis on 86 surface soil samples from northern Borneo, in addition to core NS07-25 from the southern South China Sea (SCS). The results reveal that the principal pollen component of the modern soil in northern Borneo is ferns (95.19%) and the second one is trees (4.07%). Fern spores dominate the pollen diagram of tropical rainforests in Borneo. In the northeast to southwest transect, fern spores and tree pollen represent approximately 94.47% and 4.41% of the topsoil pollen, respectively. At the highest-altitude site of the northwest to southeast transect, tree pollen and Polypodiaceae spores had the highest percentages. At low altitudes, the tree pollen content was low and Microlepia spores were abundant. Based on the principal component analysis of pollen samples, components 1 and 2 are probably related to humidity and temperature, respectively, which are crucial factors influencing pollen distribution. According to the near analysis function from ArcGIS, the pollen and spores in core NS07-25 may have originated from northern Borneo, during 37.52–26 ka BP, and <15 ka BP. The pollen concentrations in core NS07-25 vary widely from 0 to 9000 grains/g and the pollen characteristics are similar to those of the modern fern spore domain in northern Borneo. This study helps to explain the relationship between regional pollen data and the paleoenvironment in the SCS region. • Fern spores dominate in the pollen diagram of tropical rain forest in northern Borneo. • Humidity and temperature can be the most important factors influencing the pollen distribution. • Pollen of NS07-25 came from north Borneo during 37.52–26 ka BP and <15 ka BP.