The invention discloses a method and a system for controlling MMC capacitor voltage balance based on dynamic hierarchical sorting, belonging to the technical field of power system digital simulation.The method of the invention comprises the following steps of: calculating the high voltage of each layer of the valve arm; Calculating the layer number of each sub-module in the valve arm, and counting the number of sub-modules of each layer according to the layer number of each sub-module; Determining a sorting layer number and a number of sorting layer input sub-modules according to the number of the valve arm input sub-modules; Determining the input or output state of the sub-modules of the sorting layer according to the sorting algorithm of the capacitor voltage balance control; Accordingto the current direction of the valve arm, determine the input or output state of the other sub-modules. The invention only need to sort the capacitance voltages of a certain lay sub-module, Comparedwith the traditional sorting algorithm based capacitor voltage balance control method which needs to sort the capacitor voltage of all sub-modules of a single valve arm, the traditional sorting algorithm based capacitor voltage balance control method can greatly improve the computational efficiency under the premise of not affecting the control effect of the traditional sorting algorithm.