The capture of carbon dioxide (CO2) 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 CO2 adsorption and separation applications. However, the adsorption and diffusion mechanisms of CO2 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 CO2 with the functionalized MOFs. In this work, a combination of molecular dynamics simulation and density functional theory calculation was performed to study CO2 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 CO2 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 CO2 uptake. The potential of mean force (PMF) of CO2 is strongest at the CO2/functionalized MOFs interface, which is consistent with the maximum CO2 density distribution at the interface. IRMOF-3 with the functionalized linker -NH2 shows the highest CO2 uptake due to the higher porosity and binding energy. Although IRMOF-5 with the functionalized linker -OC5H11 exhibits the lowest diffusivity of CO2 and the highest binding energy, it shows the lowest CO2 uptake. Accordingly, among the five simulated functionalized MOFs, IRMOF-3 is an excellent CO2 adsorbent and IRMOF-5 can be used to separate CO2 from other gases, which will be helpful for the designing of CO2 capture devices. This work will contribute to the design and screening of materials for CO2 adsorption and separation in practical applications.