A method and an apparatus for optimizing a user plan operation in a wireless communication system based on carrier aggregation are provided in the present invention. Firstly, a user equipment receives a downlink carrier component removal signaling from a base station, the downlink carrier component removal signaling is used to indicate a removed downlink carrier component; then, the user equipment, according to the received downlink carrier component removal signaling, stops the pending HARQ procedures of the removed downlink carrier component and flushes the HARQ receiving buffer related to the removed downlink carrier component and/or stops a re-ordering procedure and/or generates a status report and sends the status report to the base station, wherein the status report is used to indicate the base station to perform retransmission and inform the base station of the data needed to be retransmitted. By applying the technology scheme of the present invention, the user plan operation at the user equipment side can be optimized, when a downlink carrier component is de-activated or de-configured.