•Aliens established across green spaces with greater proportions in artificial ones.•Native and alien species richness always had positive relationships.•Urbanization had distinct effects on flora of artificial and near-natural habitats.•Establishment of aliens caused biotic homogenization in artificial habitats.•Biotic differentiation in near-natural habitats was preserved by protecting natives. Shenzhen, a new city existed for less than three decades, experienced dramatic biological invasions of alien plants resulting from the construction of urban green spaces. In an investigation of plant species from 390 plots in 186 sites across five main types of green space (public parks, forests, vegetation corridors, residential and industrial area), a total of 474 plant species, including 221 alien species (46.6%), were recorded. Our study witnessed the spread and establishment of alien species across all urban green spaces and revealed significantly greater proportions of alien species in artificial green spaces than in natural ones. Furthermore, we found the positive relationship between native and alien species richness existed across all the green spaces and was particularly prevalent in the artificial ones. Additionally, successful establishment of alien species instigated by anthropogenic disturbances and most frequent species assemblages caused biotic homogenization in the artificial habitats. In contrast, biotic differentiation in the near-natural habitats was still preserved due to a greater level of protection for native species, which showed some resistance against the establishment of alien species. Therefore, urbanization was proven distinct effects on the flora of artificial and near-natural habitats, coexisting in the new city.