A method and an apparatus of controlling a secondary cell (SCell) are provided. The method of controlling the SCell for new radio carrier aggregation of a user equipment includes receiving at least one of downlink control information (DCI) and a medium access control (MAC) control element (CE) from a network node, wherein the at least one of the DCI and the MAC CE indicates control a SCell, the method includes determining whether to apply or ignore the at least one of the DCI and the MAC CE, and controlling the SCell according to the determination.