The present invention relates to a method and a system for three-dimensional automatic scan based primitive, and estimates a three-dimensional model of an object from three-dimensional scan data of the object, recognizes a shape of the three-dimensional model by using fitting with at least one primitive, evaluates confidence of each of surface points of the three-dimensional model based on similarity between the at least one primitive used for shape recognition and the shape of the three-dimensional model, and scans the object in a series of views determined based on the confidence of each of the surface points, and thus, accuracy of the three-dimensional scan of the object is improved and time required for scan may be reduced.