Understanding how community phylogenetic and functional structures change over succession has gained increasing attention during the last decades, but the lack of long-term time-series data has limited our understanding of the patterns and mechanisms of these changes. This is especially the case for forest communities. Here, we used an exceptionally long-term data over 68 years to analyze the secondary succession dynamics of a subtropical forest in Southeast China. We found that community phylogenetic and functional structures showed opposite temporal trends. The mean pairwise phylogenetic distance between species increased, but the mean nearest taxon distance decreased over succession, indicating both phylogenetically distantly related and sister species co-occurred in late-successional communities. In contrast, both the mean pairwise functional distance and mean nearest functional distance between species decreased over time, and community functional structure switched from overdispersion to clustering. We further distinguished the contributions of species colonization and extinction to community structural changes. We found that the new colonists were generally more distantly related to each other and to the residents than the local extinct species, resulting in increased phylogenetic overdispersion over succession. In contrast, from a functional perspective, we found that species with more similar traits to the resident species had a greater chance to colonize but a lower chance to go locally extinct, which shifted community functional structure toward clustering. Together, our study highlights the critical role of species colonization and extinction in disentangling assembly mechanisms underlying community phylogenetic and functional structures over long-term succession.