The invention relates to a megawatt battery energy storage power station real-time power control method and a system thereof. The method includes the following steps of A), reading a total power demand of a battery energy storage power station and related operation data of the power station in real time, and conducting storing and managing on the total power demand and the operation data; B) obtaining initial power command value of battery energy storage subelements of the battery energy storage power station; C) conducting real-time diagnosis and amendment on the initial power command value of the battery energy storage subelements so as to confirm power command value to be allocated to the battery energy storage subelements; and D) after the power command value of the battery energy storage subelements is collected, outputting the power command value to the battery energy storage power station so as to achieve real-time control on the battery energy storage power station. The system comprises a communication module, a data storage and management module, a total power initial allocation control module and a real-time adjusting module. The method and the system can conveniently and efficiently achieve the aims of controlling and allocating of real-time power of a megawatt lithium ion battery energy storage power station.