Formation, evolution, and vanishing of bubbles are common phenomena in our nature, which can be easily observed in boiling or falling waters, carbonated drinks, gas-forming electrochemical reactions, etc. However, the morphology and the growth dynamics of the bubbles at nanoscale have not been fully investigated owing to the lack of proper imaging tools that can visualize nanoscale objects in liquid phase. Here we demonstrate, for the first time, that the nanobubbles in water encapsulated by graphene membrane can be visualized by in situ ultrahigh vacuum transmission electron microscopy (UHV-TEM), showing the critical radius of nanobubbles determining its unusual long-term stability as well as two distinct growth mechanisms of merging nanobubbles (Ostwald ripening and coalescing) depending on their relative sizes. Interestingly, the gas transport through ultrathin water membranes at nanobubble interface is free from dissolution, which is clearly different from conventional gas transport that includes condensation, transmission and evaporation. Our finding is expected to provide a deeper insight to understand unusual chemical, biological and environmental phenomena where nanoscale gas-state is involved.