Invasive alien plants cause major losses to native biodiversity. Nature reserves are crucial in resisting invasion, but resistance varies by habitats. To explore the variations and factors that determine invasive alien plant dispersal patterns in different habitats, we investigated abandoned land, eucalyptus plantations, and natural secondary forests in Encheng National Nature Reserve, Guangxi. Our results showed a significant decrease in invasive alien plants with increasing distance from roads in secondary forest, while there was no significant trend in the two other habitats. No significant trends were observed in the distribution of invasive alien plants within the soil seed bank in the three habitats perpendicular to the road direction. Invasive alien plant composition varied with the distance from the road and was found to be similar both aboveground and in the soil seed bank. Factors influencing invasive species composition at different road edges differed by habitats, abandoned land was affected by average human flow, average traffic flow, and distance to the village, eucalyptus plantations by pH, average human flow, native herb richness of soil seed bank, and road width, and secondary forest by road width, road grade, and native herb richness and density. Our results indicated that the secondary forest resists plant invasion better than eucalyptus plantations and abandoned land, moreover, native herbs play important roles in resisting invasive species in both secondary forest and eucalyptus plantations. To target invasive alien plants in nature reserves, prioritize the abandoned land and plantation forests based on our findings.