The qualifying query is a query definition which narrows down which data the action is triggered by. It defines certain selection criteria which must be met before the record is included in the processing. It can be used to refine the selection criteria rather than have the action triggered by every new record entered into the table.
We may want to email employees who are sick for more that three days with the start date of the absence between the start and end of this week and for which the certification has not been received, rather than every employee who has an absence record entered. Without a Qualifying Query, a workflow entry would be generated for all absence records including ones for holidays, and with no check on whether certification had already been provided.