Binary matrix optimization commonly arise in the real world, e.g., multi-microgrid network structure design problem (MGNSDP), which is to minimize the total length of the power supply line under certain constraints. Finding the global optimal solution for these problems faces a great challenge since such problems could be large-scale, sparse and multimodal. Traditional linear programming is time-consuming and cannot solve nonlinear problems. To address this issue, a novel improved feasibility rule based differential evolution algorithm, termed LBMDE, is proposed. To be specific, a general heuristic solution initialization method is first proposed to generate high-quality solutions. Then, a binary-matrix-based DE operator is introduced to produce offspring. To deal with the constraints, we proposed an improved feasibility rule based environmental selection strategy. The performance and searching behaviors of LBMDE are examined by a set of benchmark problems.