A method of controlling an operation of a wind power generation system provided with a plurality of wind turbines, in which output power of each wind turbine is supplied to an electric power system through a common interconnection node where output data of each wind turbine is obtained, where a periodic correlation between output fluctuations of adjacent wind turbines is determined by using the output data, the correlation is determined as a strong correlation when the correlation is more than two times greater than an average level of the correlation, and a phase of the output of either one of the adjacent wind turbines is shifted by a period of the strong correlation.