The capture of carbon dioxide (CO 2 ) from fuel gases is a significant method to solve the global warming problem. Metal−organic frameworks (MOFs) are considered to be promising porous materials and have shown great potential for CO 2 adsorption and separation applications. However, the adsorption and diffusion mechanisms of CO 2 in functionalized MOFs from the perspective of binding energies are still not clear. Actually, the adsorption and diffusion mechanisms can be revealed more intuitively by the binding energies of CO 2 with the functionalized MOFs. In this work, a combination of molecular dynamics simulation and density functional theory calculation was performed to study CO 2 adsorption and diffusion mechanisms in five different functionalized isoreticular MOFs (IRMOF-1 through -5), considering the influence of functionalized linkers on the adsorption capacity of functionalized MOFs. The results show that the CO 2 uptake is determined by two elements: the binding energy and porosity of MOFs. The porosity of the MOFs plays a dominant role in IRMOF-5, resulting in the lowest level of CO 2 uptake. The potential of mean force (PMF) of CO 2 is strongest at the CO 2 /functionalized MOFs interface, which is consistent with the maximum CO 2 density distribution at the interface. IRMOF-3 with the functionalized linker −NH 2 shows the highest CO 2 uptake due to the higher porosity and binding energy. Although IRMOF-5 with the functionalized linker −OC 5 H 11 exhibits the lowest diffusivity of CO 2 and the highest binding energy, it shows the lowest CO 2 uptake. Accordingly, among the five simulated functionalized MOFs, IRMOF-3 is an excellent CO 2 adsorbent and IRMOF-5 can be used to separate CO 2 from other gases, which will be helpful for the designing of CO 2 capture devices. This work will contribute to the design and screening of materials for CO 2 adsorption and separation in practical applications.