Yunnan Province, located in the southeastern margin of the Tibetan Plateau, can provide important information on how climate change was influenced by global cooling. However, its variation patterns in temperature and precipitation during the latest Neogene are not well-understood. Based on the 357 specimens assigned to 31 morphotypes of plant fossils from the upper Pliocene Ciying Formation in Yiliang County, Yunnan Province, Southwest China, paleoclimate was estimated by Leaf Margin Analysis and Climate Leaf Analysis Multivariate Program. Compared to the present climate, the mean annual temperature and coldest month temperature have not changed significantly since the late Pliocene, whereas the warmest month temperature has decreased significantly. All precipitation-related parameters have decreased, particularly winter precipitation. Combined with the climatic data of the same period in other areas of Yunnan, the western and eastern Yunnan has shown a similar pattern in temperature variation since the late Pliocene except for central Yunnan; whereas the variation in precipitation does not follow a common law except for a consistent decrease in winter precipitation. Our study reinforced the fact that under the background of global cooling and intensified monsoon systems, different areas of Yunnan exhibit different climatic responses to these changes because of their topographic heterogeneities.