A system for controlling sequential startup of hard disks applicable to an electronic system with at least a first set of hard disks and a second set of hard disks is provided. A power supply module is used to provide a first power signal to the first set of hard disks to startup the first set of hard disks. A processing module is used to receive the first power signal provided by the power supply module and perform a delaying process on the first power signal to generate a delayed power signal and perform an adjustment process to the delayed power signal to generate a second power signal for outputting to the second set of hard disks, so that the first set of hard disks and the second set of hard disks can be started up sequentially.