The present disclosure provides a method, apparatus and system for detecting structural variations. The method comprises: a management apparatus divides a test sequence according to loci of chromosomes to obtain at least two portions of detection tasks; the management apparatus sends respective detection tasks to respective detection apparatuses and activates the respective detection tasks; the management apparatus detects detection task completion situations of detection apparatuses and determines whether the number of uncompleted tasks is reduced to a preset proportion threshold of a total number of tasks; when the number of uncompleted tasks is reduced to a preset proportion threshold of the total number of tasks, the management apparatus sends, to detection apparatuses that have not yet completed detection tasks, an instruction message to kill uncompleted detection tasks; the management apparatus further divides the uncompleted detection tasks into at least two portions, sends respective detection tasks to respective detection apparatuses, and activates said respective detection apparatuses to continue to perform detection of structural variations. The technical solutions of the present disclosure are employed to sufficiently use the computer resources, quicken the detection process of structural variations of the whole test sequence, and shorten the detection duration of the structural variations of the whole test sequence.