A bi-level operation scheduling of distribution system operator (DSO) and multi-microgrids (MMGs) considering both the wholesale market and retail market is presented in this paper. To this end, the upper-level optimization problem minimizes the total costs from DSO’s point of view, while the profits of microgrids (MGs) are maximized in the lower-level optimization problem. Besides, a scenario-based stochastic programming framework using the heuristic moment matching (HMM) method is developed to tackle the uncertain nature of the problem. In this regard, the HMM technique is employed to model the scenario matrix with a reduced number of scenarios, which is effectively suitable to achieve the correlations among uncertainties. In order to solve the proposed non-linear bi-level model, Karush–Kuhn–Tucker (KKT) optimality conditions and linearization techniques are employed to transform the bi-level problem into a single-level mixed-integer linear programming (MILP) optimization problem. The effectiveness of the proposed model is demonstrated on a real-test MMG system.