The Energy Internet paradigm is the evolution of the Internet of Things concept in the power system. Microgrids (MGs), as the essential element in an Energy Internet, are expected to be controlled in a corporative and flexible manner. This paper proposes a novel decentralized robust control strategy for multi-agent systems (MASs) governed MGs in future Energy Internet. The proposed controller is based on a consensus algorithm applied with the connected distributed generators (DGs) in the MGs in the energy internet paradigm. The proposed controller’s objectives are the frequency/voltage regulation and proportional reactive/active power-sharing for the hybrid DGs connected MGs. A proposed two-level communication system is implemented to explain the data exchange between the MG system and the cloud server. The local communication level utilizes the transmission control protocol (TCP)/ internet protocol (IP) and the message queuing telemetry transport (MQTT) is used as the protocol for the global communication level. The proposed control strategy has been verified using a hypothetical hybrid DGs connected MG such as photovoltaic or wind turbines in MATLAB Simulink environment. Several scenarios based on the system load types are implemented using residential buildings and small commercial outlets. The simulation results have verified the feasibility and effectiveness of the introduced strategy for the MGs’ various operating conditions.