The effects of water-based and water film assisted methods on the hole quality of femtosecond laser layered-ring trepanning on superalloy was studied. The influence of the laser pulse repetition rate on the hole entrance/exit diameter, taper angle, hole sidewall morphology and hole sidewall roughness under different water assisted methods were compared and analyzed. The results shown that both water-based and water film assistance could improve the quality of femtosecond laser drilling, reduced the hole taper angle and the sidewall roughness, and the improvement effect of water-based assistance was more obvious. When the laser pulse energy was 80 μJ and the pulse repetition rate was 100 kHz, the quality of hole sidewall was better with water-based assistance, and the taper of the hole was reduced by 18.04% compared with that in air. With the increase of laser pulse repetition rate, the hole entrance/exit diameter and taper angle decreased firstly and then increased under the two water-assisted conditions, the changes of hole sidewall roughness were not obvious with water-based assistance, but the hole sidewall roughness with water film assistance increased continuously. The experimental results provided a reference for optimizing the water-assisted femtosecond laser drilling.