This paper investigates the effect of polarization directions on underwater femtosecond laser machining of silicon wafer. Firstly, laser ablation in liquids produces laser-induced periodic surface structures (LIPSS) on both edges of the groove. The direction of LIPSS has direct correlation with the polarization of the laser beam. Secondly, the electric field intensity distribution within the groove is analyzed by numerical simulation employing the finite-difference-time-domain (FDTD) method. The simulation and experimental results reveal that the distribution of the inter electric field intensity within the grooves varies with polarization direction. As the angle between the polarization and scanning directions decreases, the peak electric field strength and groove depth gradually increase. Finally, changing the direction of polarization of the beam affects the symmetry of the groove profile. The groove profile produced by ablation is symmetrical when the beam polarization direction is parallel to the scanning direction. By modulating and optimizing the direction of polarization, grooves with large depth and symmetrical shape can be obtained.