Surface passivation is an essential step for atomistic simulations. There can be many possible surface passivation results for a given device model, such as semiconductor devices that consist of Si, GaAs, or other materials because the bonding directions of the surface atoms may not be unique. Based on the structure analysis of the given model, a generation method with structure descriptor (SDG) is proposed for surface passivation. Compared with other existing solutions, the SDG method not only provides trimmer results, but also reduces the torsion angle energy of the model, which is preferred in the simulation of atomistic models. The efficiency of this method was validated through test results from several applications.