Urbanisation has been considered to promote exotic plant invasion. Ecophysiology predicts phenotypic variation and potential evolution following urbanisation and can be used to evaluate plant invasiveness. However, few studies have included the role of ecophysiological traits for such invasiveness in urban ecosystems. Traditional plant functional traits have been used but have their limitations. Novel approaches such as metabolomics may potentially be useful. The present study explored the invasiveness of the cosmopolitan noxious invasive plant Alternanthera philoxeroides in urban and periurban areas of a megacity city in China using both traditional leaf functional traits and novel leaf metabolome as indicators. We found that traditional leaf functional traits, including specific leaf area, nitrogen concentration, carbon:nitrogen ratio and construction costs, did not differ between urban and periurban A. philoxeroides populations. However, metabolomic profiling showed that the urban populations had an up-regulated expression of zeatin and purine, two cytokinins correlated with plant growth and a down-regulated expression of isoflavonoids, a defensive metabolite for herbivory. Leaf metabolome may, therefore, be sensitive in deciphering the facilitative effects of urbanisation on plant invasion. We also found that the urban populations of A. philoxeroides accumulated more beneficial microbes, which might enhance their invasiveness. Urbanisation likely promotes exotic plants invasion through generation of metabolites, which stimulates growth via modification of the soil microbiome. Our results indicate that leaf metabolome may be used for interpreting plant invasiveness and predicting plant invasion.