The invention proposes a method, in a carrier aggregation transmission-based radio communication network, of controlling uplink transmission of a user equipment over a plurality of secondary cells in a group of secondary cells, the user equipment being configured with a group of primary cells and at least one group of secondary cells, and the group of secondary cells belonging to the at least one group of secondary cells, wherein in the event that the group of primary cells and the at least one group of secondary cells each is configured with a time alignment timer, the method comprises the steps of: terminating the uplink transmission of the user equipment over at least one activated secondary cell in the group of secondary cells when the time alignment timer of the group of primary cells expires; in the event that the group of primary cells and the at least one group of secondary cells are configured with a common time alignment timer, the method comprises the steps of: determining whether a time alignment value of the group of secondary cells is valid when the time alignment timer is in operation; and if not, terminating the uplink transmission of the user equipment over the at least one activated secondary cell in the group of secondary cells and transmitting a notification message to a base station.