Abstract: In this paper, an alien epidemic stalk-based ulcer disease of rapeseed was used as an example to propose an assessment methodology for the potential loss caused by an alien organism of unsuccessful invasion. According to the GARP niche model based on ArcGIS raster data map, the distribution areas of each adaptable variety in the provinces surveyed were extracted by the mask tool-Extract By Mask. The construction of an assessment model for the potential loss was attempted, that is, an assessment methodology for the potential loss caused by alien invasive organism was constructed from three aspects: potential direct economic loss (loss of agricultural output value, loss of agricultural and sideline food processing industry, prevention and control costs), potential indirect economic loss (rapeseed tourism industry) and potential non-economic loss (loss of ecosystem function). This research shows that the total potential loss of stalk-based ulcer disease of rapeseed was estimated at as high as 9.605 billion RMB, and the potential direct economic losses, potential indirect economic losses, and potential non-economic losses accounted for 54.9%, 36.0%, and 9.1% of the total potential losses, respectively. This research concluded that animal and plant quarantine plays an important role in preventing the invasion of alien organisms.