Crofton weed is a noxious invasive weed worldwide. However, the mechanisms underlying its invasiveness are still not well understood. We hypothesize that genetic differentiation and plasticity may help the plant invade heterogeneous habitats. To test this hypothesis, we compared the differences in seed morphometric and germination traits among 14 populations of the plant located at different elevations (640–2,430 m) in south Yunnan Province of southwest China. Germination capacity (GC) and index (GI) were markedly different among the 14 populations at the same temperature or water treatment. The results indicated genetic differentiations in these traits; maternal effects were not excluded. GC and GI were also different for each population across temperature or water treatments, showing phenotypic plasticity. Croton weed seed size and weight also responded genetically or plastically (or both) to different elevations. Seed width, weight, GC, and GI at each temperature increased with the increase of the elevation of origin, showing clinal variation patterns that reveal local adaptations to habitats encountered by the plant. The large seeds, high GC, and high GI could improve emergence, establishment, growth, and survival of seedlings at high elevation; the low GI could prevent seed germination before the onset of the rainy season at low elevation. On the basis of the results, genetic differentiation and plasticity in seed size and germination traits may help crofton weed acclimate to different elevations, facilitating its invasiveness.