The invention discloses a point cloud registration method with a low overlapping rate. The point cloud registration method comprises the following steps: step 1, obtaining a source point cloud and a target point cloud; step 2, performing downsampling by using the obtained source point cloud and target point cloud to obtain a point cloud A and a point cloud B respectively; step 3, respectively segmenting the point cloud A and the point cloud B into a plurality of local areas; step 4, performing preliminary matching, and selecting a corresponding four-point congruent set is through a 4PCS algorithm; step 5, selecting the optimal transformation of the local area; step 6, constructing a matching confidence coefficient of the local area, enumerating and calculating the matching condition of allthe local areas, sorting the local areas, and selecting the local area with the highest confidence coefficient; step 7, performing registration by using an LMidS sampling consistency algorithm to obtain a final rigid transformation matrix, and completing point cloud registration; According to the invention, good registration precision can be ensured under the condition of low overlapping rate.