We have designed and fabricated a TEM (transmission electron microscopy) liquid cell with hundreds of graphene nanocapsules arranged in a stack of two Si₃N_4–x membranes. These graphene nanocapsules are formed on arrays of nanoholes patterned on the Si₃N_4–x membrane by focused ion beam milling, allowing for better resolution than for the conventional graphene liquid cells, which enables the observation of light elements, such as atomic structures of silicon. We suggest that multiple nanocapsules provide opportunities for consecutive imaging under the same conditions in a single liquid cell. The use of single-crystal graphene windows offers an excellent signal-to-noise ratio and high spatial resolution. The motion of silicon nanoparticles (a low atomic number (Z) material) interacting with nanobubbles was observed, and analyzed, in detail. Our approach will help advance liquid-phase TEM observations by providing a straightforward method to encapsulate liquid between monolayers of various 2-dimensional materials.