The disclosure discloses a multi-time-scale reliability evaluation method of a wind power IGBT considering fatigue damage and a system thereof. Lifetime information of a power device is comprehensively extracted by using multiple time scales. An electro-thermal coupling model of an IGBT module is established to obtain a junction temperature data. A steady-state junction temperature database of the IGBT in different aging states is established. Based on a SCADA monitoring data, the junction temperature data is outputted in real-time through the electro-thermal coupling model and a real-time thermal stress cycle number is calculated in a short-term time-scale profile, and a wind speed probability distribution curve is obtained in a long-term time-scale profile. A maximum thermal stress cycle number that the IGBT can withstand in different aging stages is obtained in advance and a cumulative damage degree and an estimated lifetime of the IGBT of the wind power converter are calculated.