The invention provides a control method of wind power system operation based on wind power prediction uncertainty. The method comprises the steps of inputting basic database related to a grid of a running reserve to-be-determined time, carrying out convolution calculation of conventional unit rate probability distribution and conventional unit total rate probability distribution to obtain a capacity outage probability table (COPT) of a conventional unit, calculating the probability distribution of the sum of conventional unit total rate and wind power rate according to the capacity outage probability table (COPT) of the conventional unit, calculating the probability distribution of the difference between wind power system total rate and a load and obtaining wind power system generation margin probability distribution, obtaining the function expression between risk indication EENS and needed reserve capacity R through a curve fitting method based on system power generation margin probability distribution, and calculating a wind power system minimum reserve requirement.