The objective of the present study is the depth and layout optimizations of a single layer, high level radioactive waste repository in a discontinuous rock mass with special joint set arrangements. A single layer repository model, considering variations in the repository depths, pitches, and tunnel spacings, is used to analyze the thermomechanical interaction behavior. It is assumed that the repository is constructed in saturated granite with joints; the PWR spent fuel in a disposal canister is installed in a deposition drift which is then sealed with compacted bentonite; and the backfill material is filled in the repository tunnel. The decay heat generated by the high level radioactive wastes governs the thermomechanical behavior of the near field rock mass of the repository. The temperature and displacement behavior of the repository is influenced more by the pitch variations than the tunnel spacing and repository depth. However, the stress behavior is influenced more by the repository depth variations than the pitch and tunnel spacing. For the final selection of the tunnel spacing, pitch, and repository depth, other aspects such as the nuclide migration through a groundwater flow path, construction costs, operation costs, and so on should be considered.