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While bulk-sized metal–organic frameworks (MOFs) face limits to their utilization in various research fields such as energy storage applications, nanoarchitectonics is believed to be a possible solution. It is highly challenging to realize MOF nanobubbles with monocrystalline frameworks. By a spatially controlled etching approach, here, we can achieve the synthesis of zeolitic imidazolate framework (ZIF-8) nanobubbles with a uniform size of less than 100 nm. Interestingly, the ZIF-8 nanobubbles possess a monocrystalline nanoshell with a thickness of around 10 nm. Under optimal pyrolytic conditions, the ZIF-8 nanobubbles can be converted into hollow carbon nanobubbles while keeping their original shapes. The structure of the nanobubble enhances the fast Na+/K+ ion intercalation performance. Such remarkable improvement cannot be realized by conventional MOFs or their derived carbons.