This study investigated the enhancement effect of N₂- and Air-nanobubble water (NBW) supplementation on two-stage anaerobic digestion (AD) of food waste (FW) for separate production of hydrogen and methane. In the first stage for hydrogen production, the highest cumulative H₂ yield (27.31 ± 1.21 mL/g-VSₐddₑd) was obtained from FW + Air-NBW, increasing by 38% compared to the control (FW + deionized water (DW)). In the second stage for methane production, the cumulative CH₄ yield followed a descending order of FW + Air-NBW (373.63 ± 3.58 mL/g-VSₐddₑd) > FW + N₂-NBW (347.63 ± 7.05 mL/g-VSₐddₑd) > FW + DW (300.93 ± 3.24 mL/g-VSₐddₑd, control), increasing by 24% in FW + Air-NBW and 16% in FW + N₂-NBW compared to the control, respectively. Further investigations indicate that different gas–NBW may positively impact the different stages of AD process. Addition of N₂-NBW only enhanced the hydrolysis/acidification of FW with no significant effect on methanogenesis. By comparison, addition of Air-NBW promoted both hydrolysis/acidification stage and methanogenesis stage, reflecting by the enhanced activities of four extracellular hydrolases at the end of hydrolysis/acidification and coenzyme F₄₂₀ at the end of methanogenesis, respectively. Results from this work suggest the potential application of Air-NBW in the two-stage AD for efficient renewable energy recovery from FW.