Scorodite (FeAsO4·2H2O) is an ideal material for the fixation of arsenic that has attracted considerable research interest in recent decades. However, the position of the H atom in the scorodite crystal structure, water molecular configuration, surface morphology, and chemical state of the surface atoms have not been reported. In this work, density functional theory (DFT) is used to optimize the scorodite crystal structure, and the atomic bonding is analyzed. At the same time, a surface model is constructed to calculate the configuration and electronic structure of the surface atoms for different coordination groups. The results show that the tetrahedral [AsO4] and octahedral [FeO4(2H2O)] groups in the scorodite crystal structure have good stability(geometry configuration), and the covalent bond strength between the As atom and the bridged oxygen atom (Ob) is greater than that between the Ob atom and the Fe atom. The water molecules in the crystal structure do not seriously deform and ionize. The configuration of the water molecules remains stable through electrostatic interactions (Ow-Fe) and hydrogen bonding (H-Ob). The Fe atoms on the surface of scorodite can coordinate with OH and H2O, while the As atoms can only form a stable coordination with OH. When an Fe atom on the surface coordinates with two H2O atoms, the Fe atom will shrink to the inside of the bulk. With the increase in the hydroxylation number of the Fe atom, the bonding strength between the Fe atom and the Ob atom decreases. Different surface configurations do not affect the stability(geometry configuration) of the [AsO4] structure. In addition, the surface water molecular layer has a very weak effect on the surface coordination configuration. By contrast, in the surface configuration of the (W + OH) structure, the change in the surface atomic layer spacing is the smallest.