A fault handling method and apparatus for a wind power generator set, and a computer readable storage medium. The fault handling method comprises: dividing faults of a wind power generator set into groups according to a target protection object, each group of faults including a plurality of process faults associated with the target protection object and a target fault of the target protection object (101); if any one of the plurality of process faults in the same group as the target fault satisfies a corresponding process fault trigger condition and the target fault does not satisfy the corresponding target fault trigger condition, performing a fault-tolerant operation on the wind power generator set (102); if the target fault satisfies the corresponding target fault trigger condition, selecting, from the triggered process faults in the same group as the target fault, the process fault having the highest degree of association as a real fault that has caused shut-down of the wind power generator set (202). Thus, the invention can improve the reliability of a fault protection mechanism for a wind power generator set, and improve the accuracy of fault identification for a wind power generator set.