The work aims to propose a binocular stereo size measurement method based on the improved surf registration algorithm for the non-contact automatic measurement of packaging box in the transportation of logistics industry. Firstly, binary FREAK descriptor was used to replace the traditional SURF descriptor, which solved the shortcomings of calculation time-consuming, the generation of description vector depending on the main direction of feature, and the main direction calculation error enlarging the conduction in the following steps in the traditional SURF descriptor. Secondly, PROSAC was used to delete the mismatching points, and the FREAK cascade matching method was employed to further improve the matching speed and accuracy of the algorithm. Finally, the accurate 3D volume was obtained by disparity optimization and edge extraction algorithm to realize non-contact dimension measurement. The experimental results showed that the improved algorithm could quickly extract image feature points and match them accurately. The detection results of different packaging boxes showed that the measurement method based on the improved algorithm had small measurement error and fast detection speed. The improved image matching algorithm can effectively improve the image matching accuracy and reduce the measurement time, which is of great significance to improve the transportation efficiency and reduce the labor cost in the logistics industry.