Optimization of the Multiple Hypotheses Solution Separation (MHSS) method which has become a popular choice in civil aviation for Receiver Autonomous Integrity Monitoring (RAIM) is studied in this paper. Redistributing the integrity risk onto each hypothesis to reduce the final integrity result were the target for previous methods, the optimization process in this paper is developed from a different perspective where a new weight matrix for estimation is designed. The idea is borrowed from another optimization method, NIORAIM, which was applied in classical RAIM to improve integrity results. In this study, the design of the weight matrix is adapted for real time applications and applied in the MHSS method. Simulation results have shown that the new optimization has better performance in regards of integrity and service availability. Two major disadvantages of this method are also discussed which are the decrease of the solution precision and the increase of the computation time. It is concluded that this method is applicable for applications with more stringent requirement for integrity and relaxed requirement for precision or computation time.