Metal-organic frameworks (MOFs), which are porous crystal materials with a large surface area and high porosity, have been extensively studied. MOF derivatives with complex structures, including hollow, porous, core-shell, yolk-shell, multi-shell, and array structures, have garnered significant attention in the fields of energy, environment, and other areas due to their exceptional stability, electrical conductivity, and abundant metal active centers. The synthesis strategies, chemical structures, and various potential applications of MOF derivatives with different special structures in recent years are summarized in this review. The formation mechanisms of MOF derivatives with complex structures are described in detail, including Ostwald ripening, soft/hard template, ion exchange, selective etching, and thermally induced strategies. The practical applications of MOF derivatives in Li/Na/K ion batteries, Li-S batteries, air batteries, supercapacitors, hydrogen evolution reaction, oxygen evolution reaction, oxygen reduction reaction, hydrogen oxidation reaction, and photocatalysis are discussed and highlighted in detail. The challenges and improvement strategies for complex architectures in the future are also anticipated.