Many studies have revealed that confined water chain flipping is closely related to the spatial size and even quantum effects of the confinement environment. Here, we show that these are not the only factors that affect the flipping process of a confined water chain. First-principles calculations and analyses confirm that quantum tunnelling effects from the water chain itself, especially resonant tunnelling, enhance the hydrogen bond rotation process. Importantly, resonant tunnelling can result in tunnelling rotation of hydrogen bonds with a probability close to 1 with only 0.597 eV provided energy. Compared to sequential tunnelling, resonant tunnelling dominants water chain flipping at temperatures up to 20 K higher. Additionally, the ratio of the resonant tunnelling probability to the thermal disturbance probability at 200 K is at least ten times larger than that of sequential tunnelling, which further illustrates the enhancement of hydrogen bond rotation brought about by resonant tunnelling.