Employing the 3-dpoint cloud model of the wheat plant as the research object, through the establishment of mapping algorithm from the screen pixel to the coordinate point of the wheat plant body surface, this paper realized the calculating for the point coordinates on the wheat plant surface utilizing the mouse operation. This algorithm was constituted of solving a user view equation of given screen pixels, screening the point cloud near the line of sight, extracting the efficient point sets near the line of sight, surface fitting efficient point set and solving the intersection of the line of sight and the fitting surface five processing flow on the basis of scattered point cloud data preprocessing and rendering. Adopting the mark function of the FastSCAN 3-d digital scanner accessory instrumental software, the comparison validation of the wheat plant body surface coordinates points’ selection was conducted. The validation results show that the error less than 2.1 mm and had good precision. Considering the influence of the users’ perspective to the calculation of the plant surface points coordinates, the comparison validation was conducted with the10°, 20° and 0° perspective respectively. The results show that the error is less than 1.8 mm and had good accuracy. The mapping algorithm between the screen pixel and the object surface coordinate point established in the study could map the action of the mouse on the screen window to the operation of the object surface. Moreover, it also provided the technical reference for the establishment of the geometry measurement of the interactive plants based on point cloud data.