Three auto-aligning methods are designed,which are called the half value method, the barycenter one and the one based on genetic algorithm (GA),respectively.The auto-aligning system model is completed. Taking single mode fiber as standard waveguide,the experiment and the results show the average end-coupling losses are less than 0.1 dB,and the standard deviations are less than 0.012 dB at the wavelength 1310 nm and 1550 nm,respectively.This process only needs 2 minutes.When it comes to the experiment of fiber-SiO_2 waveguide,the results suggest the average end-coupling losses are not more than 0.15 dB,and the standard deviations are less than 0.025 dB at the wavelength 1310 nm and 1550 nm,respectively.The whole process is accomplished within 8 minutes.It shows that the methods and system have good performances.