A method and controller for controlling capacitor voltage balancing in a modular direct-current to direct-current (DC/DC) converter. The method comprises in each of sub-process of a voltage transitional process of a square wave for an arm: S701: identifying candidate sub-modules in a predetermined status from sub-modules in the arm; S702: obtaining capacitor voltages of the candidate sub-modules; S703: selecting at least one target sub-module from the candidate sub-modules based on the obtained capacitor voltages; and S704: generating a control signal to the at least one target sub-module in the arm so that a voltage across the arm changes gradually in the voltage transitional process. Using the above method, well-balanced capacitor voltages can be provided, which could provide a square waveform with a voltage changing gradually in the voltage transitional process at corresponding arm and at the same time meet requirements on the arm current by a soft switching. Therefore, the switching loss can be reduced even at a higher switching frequency and thus the system efficiency can be improved.