A method for reconstructing a three-dimensional model of point clouds includes following steps: a, scanning to obtain point clouds of an object required for a three-dimensional model reconstruction; b, analyzing quality of the obtained point clouds; c, computing a new scanning view based on the analyzed point clouds; d, scanning according to the new scanning view and updating the point clouds of step a based on point clouds obtained by the scanning according to the new scanning view in real time; and e, reconstructing a three-dimensional model according to the point clouds updated in real time. The invention further relates to a system for reconstructing a three-dimensional model of point clouds. The invention can realize full automatic reconstruction of a three-dimensional model and create a model of point clouds with high quality. In addition, the invention is easy to implement and can achieve high efficiency.