Formation, evolution and vanishing of bubbles are common phenomena in nature, which can be easily observed in boiling or falling water, carbonated drinks, gas-forming electrochemical reactions and so on. 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 the liquid phase. Here, we demonstrate for the first time that the nanobubbles in water encapsulated by graphene membrane can be visualized by in-situ ultra-high vacuum transmission electron microscopy. Our microscopic results indicate two distinct growth mechanisms of merging nanobubbles and the existence of a critical radius of nanobubbles that determines the unusually long stability of nanobubbles. 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.