The invention discloses an uplink transmission method and apparatus in a carrier aggregation system and relates to the field of radio communications so as to address the issue of how to perform uplink transmission in a secondary cell when a base station configures a user equipment additionally with the secondary cell. In the invention, a user equipment selects, under a preset reference carrier selection rule, one of downlink carriers corresponding to cells having already established downlink synchronization with a base station as a timing reference downlink carrier used by a secondary cell after the base station configures the user equipment additionally with the secondary cell; and the user equipment performs uplink transmission in the secondary cell according to downlink timing of the timing reference downlink carrier. With the invention, a timing reference downlink carrier used by an additionally configured secondary cell in uplink transmission can be determined and uplink transmission can be further preformed over the timing reference downlink carrier.