Partitioning large-scale smart distribution systems into multiple microgrids (MG) are considered an effective solution to maintain system reliability and to improve the power system restoration under emergency conditions. The partitioning planning process faces many challenges especially if the uncertain nature of both renewable energy resources (RERs) and loads, and the unbalanced operation of the distribution systems are considered. In this paper, the active distribution system partitioning is handled through a proposed three stages method. The proposed method presents a parallel planning for both energy sources integration process and partitioning process, taking into consideration all the circumstances that the system is exposed to, with determining the optimal specification of the devices that will be added to the system to reach the required efficiency of the system during system partitioning and system unification. The proposed three-stage method considers the uncertainty of PV modules and wind turbines. A new criterion for modeling RERs uncertainty is developed. Four phases for uncertainty