Tuning the activity and selectivity of metal nanoparticles (NPs) is a long-term pursuit in the field of catalysis. Herein, we report successfully improving both the activity and chemoselectivity of Pd NPs (1.1 nm) with triphenylphosphine (PPh3) cross-linked in the nanopore of FDU-12. The electron-donating effect of PPh3 increases the surface electronic density of Pd NPs and weakens the Pd–H bond, as evidenced by the results of XPS, in situ FT-IR adsorption of CO, and H2–D2 exchange reactions. Consequently, Pd NPs modified with PPh3 obtain >99% selectivity to 1-phenylethanol in acetophenone hydrogenation and 94% selectivity to styrene in phenylacetylene hydrogenation. Furthermore, the activity of Pd NPs is enhanced and suppressed by PPh3, respectively, in the hydrogenation of electrophilic nitro compounds and nucleophilic carbonyl substrates. Our primary results shed some light on judiciously choosing organic ligands for modifying the catalytic performance of metal NPs toward specific chemical transformations.