Indochina, as a global biodiversity hotspot, offers the potential for understanding the evolution of biodiversity. However, the historical narrative of plant diversity in this region remains enigmatic due to limited fossil records. Here, we report a newly discovered megafossil flora from the late Miocene of the Yen Bai Basin, northern Vietnam. This megafossil flora suggests that the late Miocene vegetation in northern Vietnam comprised mixed tropical evergreen and deciduous broadleaved forest components mainly characterized by Fabaceae, Fagaceae, and Lauraceae bearing strong resemblance to the modern vegetation in northern Vietnam. Paleoclimate reconstruction for this plant fossil assemblage using the Coexistence Approach indicates a mean annual temperature (MAT) of 18.5–23.0 °C and a mean annual precipitation (MAP) of 1183.1–2078.5 mm. Similarly, employing the Climate-Leaf Analysis Multivariate Program yields an MAT of 21.3 ± 2.3 °C and a growing season precipitation (GSP) of 1328.6 ± 606.0 mm. The length of the growing season was about eleven months. Overall these results indicate a modern-like warm and humid tropical monsoon climate in northern Vietnam during the late Miocene. Climatic comparison of the Yen Bai with other fossil floras in northern Vietnam and southern China reveals the relative stability of temperature seasonality since the middle Eocene but obvious long-term variation in precipitation seasonality, particularly in respect of precipitation during the three consecutive driest months (X3.DRY). This suggests the Asian monsoon in northern Vietnam underwent important changes from the middle Eocene to the late Miocene, and intensified significantly during the middle and late Miocene. Our results show the modernization of plant diversity in northern Indochina had its origin in the Paleogene and further developed in the late Miocene, and was linked to the evolution of the Asian monsoon mainly in terms of changes in dry season precipitation.