For chemical warfare agent removal, the humidity emerges as an unavoidable challenge that significantly affects the performance of metal–organic frameworks. In this work, via density functional theory calculations, ab initio molecular dynamics and classical molecular dynamics simulations, we investigate the structural and diffusion properties of water in the pristine defect‐free UiO‐66, one Zr‐based metal–organic framework. Through the detailed analyses of the distribution probability of water in two different cages of UiO‐66, the binding interaction between water and UiO‐66, the hydrogen bonding networks and resulted localized water clusters, we gain a fundamental understanding of structural and dynamics properties as well as the concentration dependence of water in UiO‐66. We anticipate those theoretical results could provide insight to the competitive adsorption of water and chemical warfare agents, which eventually shows the utmost importance for the design and development of the next generation porous materials with appropriate water properties in real‐life applications.