A method and apparatus are disclosed, from the perspective of the UE (User Equipment). In one embodiment, the method includes maintaining a first timing advance value for uplink transmissions. In addition, the method includes receiving a signaling, via a downlink control channel, to schedule a first uplink transmission in a cell, wherein the signaling includes a first information to assist the UE to determine a specific timing advance value for the first uplink transmission, and the first information indicates an index value used to control an amount of timing adjustment to be applied. The method also includes performing the first uplink transmission in the cell at transmission timing determined at least based on the specific timing advance value.