The site dose rate of a spent-fuel storage facility to the populace is a major concern in a radiation protection project. Shielding analysis of the facility must be performed to ensure that the nearby dose rates are within regulation limitations. The purpose of this study was to simulate an independent spent-fuel storage installation (ISFSI) storage facility with different methods and different conditions for validation and analysis. The discrete ordinates code DORT and the SKYSHINE III code were used for the cask surface flux estimation and the site dose rate calculation, respectively. The Monte Carlo code MCNP was also utilized to estimate the surface dose rate and site dose rate by its subsequent calculation. Various cask decay heats (23, 14, and 7 kW/cask) were considered as the source conditions. A facility layout composed of 30 casks was also simulated by the MCNP code and analyzed for the cask self-shielding effect to a certain detecting point. For a single storage cask, comparisons of the site dose rates calculated by different methods were carried out at variant distances. For the layout simulation, the calculated results indicated that the self-shielding effect could be roughly classified into several groups according to the location of the storage cask, and a factor could be assigned to each group. These classified factors might help to infer the site dose in variant layout designs. The site dose rates calculated by different codes were compared for the whole facility, too. In spite of the similar dose rates on the cask surface, the difference of site dose rates changes with decay heat. The layout study of the ISFSI facility could offer information to make the site dose estimation more efficient as many layout assessments are needed.