Based on analysis of the coupling theory, the two auto-aligning methods and programs are designed. Experiment results using single mode fiber as standard waveguide show that the average end-coupling loss is 0.075 dB, the standard deviation is 0.0099 dB at the wavelength 1310 nm, and is 0.0062 dB and 0.0066 dB at 1550 nm, respectively. A process only needs 2 min. When it comes to fiber-SiO2 waveguide-fiber system, the average end-coupling losses are 0.140 dB and 0.109 dB, and the standard deviations are 0.0082 dB and 0.0107 dB, at 1310 nm and 1550 nm, respectively. The whole process is accomplished within 8 min.