The invention relates to a wind power generation system and a control method thereof, in particular to a variable frequency type three-phase wind power generation system and a control method thereof. The variable frequency type three-phase wind power generation system comprises a master control part, a rectification circuit, an inverter circuit, a detection circuit, a storage battery charging and discharging circuit, a storage battery interface, a wind power generator interface, a power frequency load interface, a variable frequency load interface, an electronic control switch, a warning answering device, and an optional isolation transformer. The control method comprises the following steps: before the variable frequency load is electrified, on the premise that all power frequency loads are allowed to be powered off, all power frequency loads are disconnected and forbidden to be switched on, and the variable frequency load is electrified in a variable frequency mode; when the frequency is changed into a constant power frequency, a system automatically electrifies the power frequency loads which are allowed to be electrified one by one by referring to the advanced setting of a user, wherein the power sum of the power frequency loads is not more than the residual power generation capacity of the system. For the wind power generation system containing the motor type load, the installed capacity of the wind driven generator is reduced at the beginning of the scheme design by the invention, and the cost is lowered.