Bio-invasion has caused serious ecosystem damage and enormous economic losses in China, and it has been the greatest factor to island bio-diversity reduction. Xiamen, as an important seaport with a relatively high conservation value, is particularly vulnerable to bio-invasion for its typical island ecosystem as well as frequent human-made disturbance. As a result of field surveys, literature review, and consultation with experts, a list of 67 alien plants identified as major invaders (12 species) and emerging invaders (55 species) in Xiamen has been compiled. Based on the analysis of the current situation of bio-invasion in Xiamen, a risk assessment system for alien plant invasion has been designed using a ranking system and an analytic hierarchy process. The system consists of 17 secondary indices, grouped into 6 primary indices reflecting the different stages in the bio-invasion process: introduction, establishment, dispersion, current range, infestation, and artificial control. Biogeographical, ecological, and experience-linked aspects of the species as well as artificial disturbance were taken into account in the index selection and criterion development. The system was then validated (and worked well) using fifty well-known alien plant species as candidates. Appropriate recommendations are proposed to help local policy-makers prioritize their decisions on such alien plants.