Ibuprofen (IBP) and naproxen (NAP), two typical anti-inflammatory drugs, were frequently detected in natural waters. Therefore, their adsorption to various materials has drawn great interests. However, the adsorption mechanisms of IBP and NAP at a molecular level were not well-known. This study investigated the adsorption of IBP and NAP by two types of metal organic frameworks (MOFs), UiO-66 and UiO-66-NH2, and the adsorption mechanisms were revealed at macro and micro molecule levels based on experiments and density functional theory (DFT) calculations. Greater adsorption of IBP onto MOFs was observed compared with NAP, which is incurred by its higher binding energies with adsorbents than NAP as revealed by DFT calculations. Four mechanisms, including pi-pi EDA interaction, Lewis acid/base complexing (LAB), hydrogen bonding, and anion-p interaction, were simultaneously involved in the adsorption of IBP/NAP by MOFs. The binding energies followed the order of pi-pi > hydrogen bonding > LAB > anion-p. The decreasing adsorption of IBP and NAP with rising pH was induced by the facilitated aggregation of MOFs at pH < pHpzc and the electrostatic repulsion between IBP/NAP and MOFs at pH > pHpzc. Direct competition for adsorption sites accounted for the competitive adsorption between IBP and NAP, and the extra type of binding site (amino group) and less amount of adsorption sites induced the less competition between IBP and NAP onto UiO-66-NH2 compared with UiO-66. This study, at a molecular level, provides adsorption mechanisms of acidic pharmaceuticals with MOFs.