The present disclosure discloses a method for processing a measurement task in a carrier aggregation system, which includes: deleting all measurement tasks related to a source Secondary Cell (Scell); or deleting a measurement task related to an Scell in a deleted source Scell; or doing not delete a measurement task related to the source Scell when a source Scell is reassigned to another frequency having a measurement object, and modifying a measurement object corresponding to the measurement task related to the source Scell to a measurement object of the reassigned frequency. When a source Pcell and a target Pcell are on different frequencies and the measurement object corresponding to the measurement task is a frequency on which there is the source Pcell when the frequency on which there is the target Pcell is the measurement object, the measurement object is modified to a measurement object of the frequency on which there is the target Pcell; and when the measurement object corresponding to the measurement task is the frequency on which there is the target Pcell, the measurement object is modified to a measurement object of the frequency on which there is the source Primary Cell (Pcell). The present disclosure further discloses a system for processing a measurement task in a carrier aggregation system. The present disclosure effectively decreases a configuration signaling of a measurement task and increases a utilization rate of the air interface resource.