In the deregulated power environment, including Central operator (CO) and Micro Grids (MGs), different parts of the network are dedicated to the private sector, and each of them seeks to increase their profits independently. The CO and MGs should cooperate and collaborate in terms of operating, security and reliability in the whole power system. This article proposes a new method based on a System of System (SoS) concept for the secure and economic hourly generation scheduling to find optimal operational point. The main methodology includes three steps. In the first step, the power system is divided into several subsystems by using a spectral clustering partitioning technique to reduce converge time by decentralizes methods. And also load forecasting based on a Gaussian probability distribution function to avoid conventional calculation and considering uncertainty of the loads has been presented. To find a similar scenario, and reduction scenario with low probability, the probabilistic method has been addressed. The main contribution of this method is removing scenarios with low value of probabilities and scenarios which are similar to each other. In fact, the reduced set must include scenarios which are scattered appropriately in the uncertain space while holding high probabilities. In order to estimate the similarity (distance) between two scenarios the Kantorovich distance is implemented. In the second step, the hierarchical Bi-level optimization approach is used to execute the decentralized decision making to solve the Security Constraints Unit Commitment (SCUC) problem between CO and MGs. Regarding all physical relations and shared data among CO and MGs, the SoS concept and Bi-level optimization are presented to find the optimal operating point of autonomous systems. In the third step, a random number of generators will be select. Hence, the initial iteration number is set. In this step, sampling from state space to classifying reliability object achieved (The expected energy not supplied and loss of load probability are the reliability criterion). The presented method is evaluated using a 6-bus, the RTS 24-bus, 118-bus, and 4672-bus as an IEEE test systems. The suggested structure has been implemented by GAMS, and the results illustrate the usefulness of the presented methodology. To comparing proposed approach with the centralized method, the results illustrate improving total operational costs and security (in RTS-24($603,209), 118 bus ($2 562 154) and 4672-bus ($9 185 168)) in scenario 3 near to 9%, 10% and 8% respectively. Similarly, by comparison (in three test systems) with genetic algorithm these improvements are near to 23%, 22% and 13% respectively.