In this paper, an adaptive concept of virtual generator (VG)‐based controller is presented for dynamic stability of stochastically‐modeled microgrids consisting of low inertia resources. For this purpose, considering a set of energy storage systems (ESSs) dispatched in the network, a controlled islanding scheme (CIS) is provided to dynamically control the microgrid frequency. In this context, based on the concept of center of inertia (COI), the proposed VG scheme is developed through mathematical formulation. Inter‐area torques evaluated by microgrid control areas in the COI frame are used as input signals of the developed VG‐based controller. Also, for the ESSs, an equivalent dispatch model is provided and developed through the microgrid dynamic model for improving frequency stability during inter‐area oscillations. The proposed VG‐based controller is an online and non‐model‐based scheme which controls several microgrid systems together as an integrated network connected to the upstream network. In order to evaluate the ability of the proposed scheme, real‐time simulations are carried out on two different test systems consisting of several microgrids. The system dynamic performances are evaluated in time‐domain simulations. Numerical results demonstrate the effectiveness of the proposed scheme in increasing system inertia constant resulting in a proper dynamic performance with a high damping ratio in facing severe inter‐area oscillations.