A method based on MATLAB instrument control technology was proposed to realize an auto-coupling system,avoiding complicated and time-consuming manual alignment. A Binary-tree Data-truncation (BTDT) algorithm and Return-traversal Search (RTS) algorithm based on a threshold were designed for single axis searching. Return-traversal algorithm provides a higher accuracy which also achieves multiple kinds of accuracy and BTDT can search faster.Combined with a laser and a power meter, an auto testing system was developed with GPIB technology. The experiments show that insertion loss of tapered fiber can drop to 8~9 dB including the transmission loss of waveguide in 15 minutes while aligning manually usually takes more than 0.5 hour and system can be kept stable in 15~20 minutes. Besides, with auto testing system, scan of wavelength and power can be completed in 8 minutes for 2 200 points. Auto-coupling system has good effect, stability and practicability.