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Abstract To investigate the role of interlayers on the growth, microstructure, and physical properties of 3D nanocomposite frameworks, a set of novel 3D vertically aligned nanocomposite (VAN) frameworks are assembled by a relatively thin interlayer (M) sandwiched by two consecutively grown La_0.7Sr_0.3MnO₃(LSMO)‐ZnO VANs layers. ZnO nanopillars from the two VAN layers and the interlayer (M) create a heterogeneous 3D frame embedded in the LSMO matrix. The interlayer (M) includes yttria‐stabilized zirconia (YSZ), CeO₂, SrTiO₃, BaTiO₃, and MgO with in‐plane matching distances increasing from ≈3.63 to ≈4.21 Å, and expected in‐plane strains ranging from tensile (≈8.81% on YSZ interlayer) to compressive (≈–6.23% on MgO interlayer). The metal‐insulator transition temperature increases from ≈133 K (M = YSZ) to ≈252 K (M = MgO), and the low‐field magnetoresistance peak value is tuned from ≈36.7% to ≈20.8%. The 3D heterogeneous frames empower excellent tunable magnetotransport properties and promising potentials for microstructure‐enabled applications.