The present invention discloses an inter-harmonics control method in a wind power collection station. The method comprises that an inter-harmonic signal extraction module carries out spectral analysis on a tie line current from the wind power collection station to a main network, calculates frequency fc of a harmonic component with the maximum amplitude, and extracts inter-harmonic signals in a tie line voltage and each wind power farm current; a wind power farm that is allowed to be cut in the collection station is determined according to the tie line inter-harmonic current, the inter-harmonic voltage, and the wind power farm inter-harmonic current; absolute values of difference values between the fc and a set of characteristic frequencies are calculated, and a minimum value dfmin among the absolute values is solved; and a sub-round and level-to-level cutting module cuts each wind power farm that is allowed to be cut in a series of rounds and level by level according to the tie line inter-harmonic current, the dfmin, and the wind power farm inter-harmonic current. According to the method disclosed by the present invention, the tie line between the wind power collection station and the main network, and each wind power farm can be monitored simultaneously, the relatively large inter-harmonic current existing in the power grid can be online monitored in real time, and whether there is an inter-harmonic generation source in the wind power collection station can be online determined in real time.