In order to achieve the large scope evaluation for micro-structures, a low overlap rate and large scope 3-D structure stitching method is presented in this paper.According to the features of micro -structures,the area for the feature points extraction is designated in the overlap region in the first step based on the experiment al configuration,in order to reduce the possibility of incorrect matching and increase the processing efficiency.Inside this special s ector,the feature points are extracted through SIFT algorithm.During the feature points matching process,the matched points search ing area is optimized based on the testing profiler parameters in order to increase the matching reliability.According to the local continuity inside the overlap region,the mismatch between the stitched structures due to the environmental disturbance during the test is corrected by a correction matrix in the last step. The comparison experiments between the proposed method and a commercial profiler are carried out,which show that the new algorithm is not only eff ective for the structure with rich features,but also applicable for the array st ructures with unobvious features.The further experiment shows that the stitching could be successfully achieved at overlap rate of 6%.