The establishment of structure–property relationships in heterogeneous catalysis is of prime importance but remains a formidable challenge. Metal–organic frameworks (MOFs) featuring excellent chemical tunability are emerging as an auspicious platform for the atomic-level control of heterogeneous catalysis. Herein, we encapsulate palladium nanoparticles (Pd NPs) in a series of isoreticular mixed-linker MOFs, and the obtained MOF-Pd NPs catalysts were used to unveil the electronic and steric effects of linker substitution on the activity of these catalysts in the Suzuki–Miyaura cross-coupling reactions. Significantly, m-6,6′-Me2bpy-MOF-Pd exhibits a remarkable enhancement in the activity compared to non-functionalized m-bpy-MOF-Pd and m-4,4′-Me2bpy-MOF-Pd. This study unambiguously demonstrates that the stereoelectronic properties of linker units are crucial to the catalytic activity of nanoparticles encapsulated in MOFs. More interestingly, the trend of activity change is consistent with our previous work on catalytic sites generated in situ from Pd(II) coordinated in MOFs bearing the same functional groups, which suggests that both MOF-Pd NPs and MOF-Pd(II) catalysts generate similar active centers during Suzuki–Miyaura coupling reactions. This work paves a new avenue to the fabrication of advanced and tunable MOF-based catalysts through rational linker engineering.