Urbanization can significantly drive biodiversity loss in river ecosystems, yet the underlying mechanisms require further study. Here, we used a trait-based approach to investigate temporal succession and variation in the dissimilarity of phytoplankton community functional traits along an urbanizing subtropical river over 11 years - during which time the downstream of catchment underwent rapid urbanization. Our results indicated that urbanization altered the interannual succession of phytoplankton. The phytoplankton communities in the rural region were mainly shaped by a specialist trade-off between extreme lotic strategies (single cell, high maximum growth rate and high silica demand) in river habitat, and extreme lentic strategies (colonial, toxin production and nitrogen fixation abilities) in reservoir habitat. Conversely, in the urban region, generalist strategies with intermediate trait combinations (moderate mobility and mixotrophic ability) dominated the communities in both river and reservoir habitats. Time-lag analysis of functional dissimilarity showed lower, or even no significant variations of functional beta diversity in the urban region. Further decomposition of functional beta diversity indicated a reduced rate of functional turnover in urban river compared with that in rural river and a decrease in functional nestedness in urban reservoir. Paired differences between river and reservoir in the urban region exhibited convergent succession by functional turnover. The convergent succession and homogenization in the urban region made the variation in phytoplankton functional structure more unpredictable in a random forest model, and diminished the relationship between functional dissimilarity and environmental factors compared to the rural region. Our study shows how urbanization shapes the phytoplankton functional structure and causes homogenization in functional trait composition. The insight gained enhance our ability to assess and predict the environmental impacts of urbanization on aquatic ecosystems.