35 surface soil samples and 28 profile soil samples were collected in Longitudinal Range-Gorge Region, Southwest China. The distribution of pollen and spores and their relationship with the environment are analyzed. The results show that there are significant differences in pollen and spores taxa, amounts, dominant taxa and florae between the eastern and western flanks of the Ailao Mountain. There are more pollen and spores taxa, a greater amount and complexity on the western flank of the mountain than those on the eastern flank, while the dominant taxa are more centralized and prominent on the eastern flank of the Ailao Mountain. As for the plant florae distribution, there are significant differences in the number of taxa and composition between the eastern and the western flanks. The analysis of profile pollen and spores assemblage shows that its trends of variation are basically in accordance with the surface pollen and spores, which are also indicators of the environmental differences between the two flanks of the mountain. These significant spatial differences of pollen and spores are very close to the regional topography and climate difference. The mountain running perpendicular to the moisture-laden air flow serves as a barrier and the monsoon circulations the east and the west of the mountain result in different energy-moisture characteristics. We conclude that the main patterns of the pollen and spores can be attributed to the environmental differences.