The creation of ‘unified composites’ from zeolites and metal–organic frameworks (MOFs) represents a promising frontier for engineering synergistic properties in applications. However, the integration of these distinct nanoporous materials to harness combined structural, compositional, and functional advantages remains a critical and unmet challenge due to their different synthetic conditions and lattice mismatches. Herein, we develop a growth-kinetics-mediated cascade assembly strategy to construct a series of hierarchically porous zeolite@MOF composites with well-defined heterogeneous hollow multi-shell architectures. A central feature of this method is the precise regulation of MOF growth kinetics on zeolite layer surfaces by constructing metastable layers that act as removable nanolinkers between the hierarchically porous zeolite and MOF shells, enabling selective etching with acetic acid to achieve integration of heterogeneous shells and simultaneous formation of interlayer voids. Dynamic regulation of the assembly process enables fine control over mesopore size, shell sequence, particle size, and shell thickness. Importantly, this strategy can be extended to prepare various hollow multi-shell zeolite@MOF composites by changing zeolite core or MOF shell. Benefiting from the integration of Brønsted and Lewis acid sites, efficient mass transfer, and enrichment effect of the hollow multi-shell configuration, the bifunctional catalysts exhibit significantly enhanced activity and selectivity in one-pot reductive etherification of 5-hydroxymethylfurfural to 2,5-bis(isopropoxymethyl)furan, a biodiesel or diesel additive. This work not only demonstrates a powerful synthetic methodology for constructing zeolite@MOF composites with highly controllable heterogeneous hollow multi-shell architectures but also provides new insights into the design of multicomponent crystalline nanoporous catalysts for various complex heterogeneous catalysis.