When applying the conventional motion estimation algorithms for sample video coding,the invalid search points will be searched redundantly and some valid points will be missed,So an asymmetrical motion estimation method with boundary constraint is proposed.Firstly,on the basis of original search scope,the motion performance of sample video in the instrument is measured and recorded with statistical method of motion parameters at fixed points.According to the statistical results,a motion boundary is set to reduce the search points.And then,in accordance with the motion feature of sample video,an asymmetrical search model with boundary constraint is brought out to optimize the search algorithm.The different sample videos from electron probe and electron microscope are employed to test the performance of the proposed estimation method.It proves that the method compresses the motion estimation time by about 33% compared with the multi-direction search(MDS) algorithm.And in terms of coding quality,it maintains and even exceeds the MDS method.