Alignment coupling between polarization maintaining fiber and input end of Y-waveguide is studied. The influence of alignment deviation on coupling loss at five degrees of freedom is simulated by mode-field overlapping integral method, and an experimental scheme based on digital image is designed. The simulation results are consistent with the experimental data, which proves the feasibility of the experimental scheme. The results reveal that the transverse misalignments X and Y have the greatest influence on the coupling loss, while the vertical spacing Z has less influence on the coupling loss. And the coupling loss generated by the deflection angle α or pitch angle β is mainly caused by additional transverse displacement, while the mere change of angle has minimal impact on coupling loss. When the coupling loss is required to be under 0.5 dB, the tolerance range of transverse misalignment and vertical spacing should be restricted within -1 μm to 1 μm and -20 μm to 20 μm, respectively. The conclusions provide references for subsequent research on automatic alignment system.