A series of defect-engineered metal-organic frameworks (DEMOFs) derived from parent microporous MOFs was obtained by systematic doping with defective linkers during synthesis, leading to the simultaneous and controllable modification of coordinatively unsaturated metal sites (CUS) and introduction of functionalized mesopores. These materials were investigated via temperature-dependent adsorption/desorption of CO monitored by FTIR spectroscopy under ultra-high-vacuum conditions. Accurate structural models for the generated point defects at CUS were deduced by matching experimental data with theoretical simulation. The results reveal multivariate diversity of electronic and steric properties at CUS, demonstrating the MOF defect structure modulation at two length scales in a single step to overcome restricted active site specificity and confined coordination space at CUS. Moreover, the DEMOFs exhibit promising modified physical properties, including band gap, magnetism, and porosity, with hierarchical micro/mesopore structures correlated with the nature and the degree of defective linker incorporation into the framework.