Precise placement of multiple functional groups in a highly ordered metal-organic framework (MOF) platform allows the tailoring of pore environment which is required for advanced applications. To realize this, we present a comprehensive study on linker installation method, in which a stable MOF with coordinatively unsaturated Zr6 clusters was employed and linkers bearing different functional groups were post-synthetically installed. A Zr-MOF with inherent missing linker sites, namely PCN-700, was initially constructed under kinetic control. Twelve linkers with different substituents were then designed to study their effect on MOF formation kinetics and therefore resulting MOF structures. Guided by the geometrical analysis, linkers with different lengths were installed into a parent PCN-700, giving rise to eleven new MOFs and each bearing up to three different functional groups in predefined positions. Systematic variation of the pore volume and decoration of pore environment were realized by linker installation, which resulted in synergistic effects including an enhancement of H2 adsorption capacities of up to 57%. In addition, a size-selective catalytic system for aerobic alcohol oxidation reaction is built in PCN-700 through linker installation, which shows high activity and tunable size-selectivity. Altogether, these results exemplify the capability of linker installation method in pore environment engineering of stable MOFs with multiple functional groups, giving an unparalleled level of control.