A method and a system for controlling a distributed power generation system are disclosed. The distributed power generation system includes N sub isolated three-port converters and N independent distributed DC power sources in a one-to-one correspondence to the N sub isolated three-port converters, N is a natural number greater than 1; an input-port of each of the sub isolated three-port converters is connected to the corresponding distributed DC power source, bidirectional-ports of the sub isolated three-port converters are connected in parallel to build a low voltage DC bus, and output-ports of the sub isolated three-port converters are connected in series and connected to a medium voltage DC distribution network. The control method comprises: controlling an input power of each of the sub isolated three-port converters independently, performing a power-voltage droop control strategy based on a virtual resistor on the bidirectional-port and the output-port to realize the stable control of the bidirectional-port voltage and the voltage sharing control of the output-port voltage of each of the sub isolated three-port converters. A modular design is realized. Thus a viable technical solution is provided for connecting the distributed power generation system to the medium voltage DC distribution network.