Display omitted •The etching rate under 40-kHz pulses are ten times higher than that under 2.5-kHz pulses.•Two etching mechanisms exist when using high-repetition-rate laser pulses.•Heat accumulation and probably surface modification cause the incubation effect.•‘Strong ablation’ causes a rough morphology, high etching rate and a phase change.•The incubation effect can be used for high quality cutting of transparent materials. Laser-induced backside wet etching (LIBWE) has been extensively studied in recent years due to its high-quality processing of transparent materials. Toxic organic solutions and ultraviolet (UV) lasers with low repetition rates are necessary in conventional LIBWE, which limits the processing efficiency and results in environmental problems. Some studies have found that near-infrared lasers can also be employed in LIBWE when aqueous solutions containing Cu2+ are used as the absorbing liquids. These new findings show dramatic enhancements in processing efficiency, but the underlying mechanisms have not been clearly identified. In this study, we found that the etching rate of LIBWE using near-infrared lasers could be increased greatly and that the processing quality deteriorated appreciably when using high-repetition-rate laser pulses. By observing the evolution of laser-induced cavitation bubbles, we identified two etching mechanisms during LIBWE when high-repetition-rate laser pulses were used and determined that the incubation effect drove the transformation between the two mechanisms. Our findings demonstrate that LIBWE using a near-infrared nanosecond laser can be used not only to obtain high-quality micro-grooves on sapphire but also to cut sapphire substrates efficiently by utilizing the incubation effect.