Spent nuclear fuel in a geological repository could be an easily accessible source of Pu for state and non-state proliferators after the level of radioactivity significantly decreases in the long term. Such concerns have been continuously raised, but little systematic analysis has been conducted to compare costs and benefits of long-term safeguards to protect Pu in spent nuclear fuel in a final repository. A system thinking model combined with game theory was developed to evaluate the costs and benefits of safeguards of the final repository. In this analysis, the safeguards system is considered as a strategic game between two competing players - a proliferation player and a safeguards player. Detailed data, such as drilling rates and costs, are carefully obtained from real world industrial applications. The costs of safeguards are predicted from the data of commercial satellite monitoring. The model is applied to two potential proliferation scenarios. One is the construction of a clandestine access tunnel using a tunnel boring machine. The other one is chemical extraction through drilling of a vertical deep borehole. The calculated costs of long-term safeguards are mapped for various decisions of the proliferation player and the safeguards player to suggest the optimized approach for the long-term safeguards of the final repository.