Chemical environment control of the metal nanoparticles (NPs) embedded in nanocrystalline metal-organic frameworks (nMOFs) is useful in controlling the activity and selectivity of catalytic reactions. In this report, organic linkers with two functional groups, sulfonic acid (-SO3H, S) and ammonium (-NH3(+), N), are chosen as strong and weak acidic functionalities, respectively, and then incorporated into a MOF [Zr6O4(OH)(4)(BDC)(6) (BDC = 1,4-benzenedicarboxylate), termed UiO-66] separately or together in the presence of 2.5 nm Pt NPs to build a series of Pt NPs-embedded in UiO-66 (Pt subset of nUiO-66). We find that these chemical functionalities play a critical role in product selectivity and activity in the gas-phase conversion of methylcyclopentane (MCP) to acyclic isomer, olefins, cyclohexane, and benzene. Pt subset of nUiO-66-S gives the highest selectivity to C-6-cyclic products (62.4% and 28.6% for cyclohexane and benzene, respectively) without acyclic isomers products. Moreover, its catalytic activity was doubled relative to the nonfunctionalized Pt subset of nUiO-66. In contrast, Pt subset of nUiO-66-N decreases selectivity for C-6-cyclic products to <50% while increases the acyclic isomer selectivity to 38.6%. Interestingly, the Pt subset of nUiO-66-SN containing both functional groups gave different product selectivity than their constituents; no cyclohexane was produced, while benzene was the dominant product with olefins and acyclic isomers as minor products. All Pt subset of nUiO-66 catalysts with different functionalities remain intact and maintain their crystal structure, morphology, and chemical functionalities without catalytic deactivation after reactions over 8 h.