A new method to identify the position of Japan Euonymus plantlets in bottle from the bottle bottom was proposed according to the appearance of plantlets in bottle. The experimental data of 200 plantlets showed that the method is feasible, for the distance between stalk and root is 1.5 mm in 97% plantlets. A set of image acquisition system for bottle bottom has been established, and the algorithm to extract the root image from the bottle bottom image, tag the area and calculate the center of each root was developed. Detecting experiments were carried out by identifying images of 240 plantlets and measuring the distances between calculated root centers and actual stalk centers. The results indicated that the detecting accuracy of root amount is 92.05% and the average distances between calculated root centers and actual stalk centers are 0.85 mm. It can meet the requirement of transplanting process.