The present invention discloses an intelligent control method that a wind power plant participates in the primary frequency modulation and a control system thereof. The intelligent control method comprises the following steps of real-timely acquiring the power grid frequency of the high-voltage end of a wind power plant main transformer, determining whether the power grid frequency exceeds a set frequency dead zone, if the power grid frequency exceeds the set frequency dead zone, representing that the wind power plant needs to participate in the primary frequency modulation; calculating an active power superpose amount delta P needing to be adjusted; before the primary frequency modulation, calculating a draught fan target value Ptotal, and classifying the lists of the draught fans capableof participating in the modulation; according to the superpose amount delta P, making an adjusting cycle number needed by a frequency modulation task, then issuing the instructions of a first adjusting cycle to the wind turbine generator sets; monitoring the execution situations of the wind turbine generator sets, feeding back to an energy management platform, arranging a wind turbine generator optimal execution list to issue the instructions of a second adjusting cycle, and so on, finishing a primary frequency modulation task. According to the present invention, the instructions are issued in twice, the instructions at the first time are the tentative instructions, and by synthesizing the feedback information, the second time instructions are issued, so that the adjustment precision is higher.