Ensuring the secure and cost-effective operation of smart power microgrids has become a significant concern for managers and operators due to the escalating damage caused by natural phenomena and cyber-attacks. This paper presents a novel framework focused on the dynamic reconfiguration of multi-microgrids to enhance system’s security index, including stability, reliability, and operation costs. The framework incorporates distributed generation (DG) to address cyber-attacks that can lead to line outages or generation failures within the network. Additionally, this work considers the uncertainties and accessibility factors of power networks through a modified point prediction method, which was previously overlooked. To achieve the secure and cost-effective operation of smart power multi-microgrids, an optimization framework is developed as a multi-objective problem, where the states of switches and DG serve as independent parameters, while the dependent parameters consist of the operation cost and techno-security indexes. The multi-objective problem employs deep learning (DL) techniques, specifically based on long short-term memory (LSTM) and prediction intervals, to effectively detect false data injection attacks (FDIAs) on advanced metering infrastructures (AMIs). By incorporating a modified point prediction method, LSTM-based deep learning, and consideration of technical indexes and FDIA cyber-attacks, this framework aims to advance the security and reliability of smart power multi-microgrids. The effectiveness of this method was validated on a network of 118 buses. The results of the proposed approach demonstrate remarkable improvements over PSO, MOGA, ICA, and HHO algorithms in both technical and economic indicators.