A method for computing minimum distances between two point clouds is provided. The method includes: (a) acquiring a first point cloud and a second point cloud; (b) establishing a topological structure for the second point cloud to make points of the second point cloud confined in a plurality of related cubical grids; (c) selecting a point from the first point cloud; (d) searching one or more cubical grids from the related cubical grids according to the topological structure and computing a distance between the selected point and each of points which belong to the second point cloud and in the searched cubical grids to obtain a closest point from the second point cloud, which has a shortest distance to the selected point; (e) repeating steps from (c) to (d) until all the points in the first point cloud have been selected. A related system is also provided.