The micropore range of typical MOFs limits the accessibility of substances e.g., dyes have larger sizes. In this work, MIL-121 was transformed into hierarchically porous MOF variants through temperature-regulated linker thermolysis, of which hierarchical porosity (increased average pore size of up to 61.8 Å) and increased specific surface area of up to 346.2 m2/g were achieved. Surface functionality of –COOH and anhydride groups were also improved together with the formation of defective sites and graphite carbon with π-conjugated layers. Improved adsorption of CR and MB were observed with the thermally treated variants, in particular for MIL-121-500 (597.9 and 246.0 mg/g, respectively), when compared with pristine MIL-121 (69.7 and 27.8 mg/g, respectively). Pseudo-second order and Langmuir models were used to explain the adsorption mechanisms. Thermodynamic studies revealed the adsorption of CR and MB on MIL-121-500 were spontaneous, and were endothermic and exothermic, respectively. Characterization of the adsorbents and the DFT calculations demonstrated the synergetic effect of the improved textural and functional properties (especially the oxygen defective sites) of MIL-121-500 was responsible for the enhanced adsorption of dyes. This work sheds light on improving the adsorption performance of MOFs to organic dyes through linker thermolysis and offering a systematic approach to designing custom-built MOFs for targeted applications.