A deactivation method and apparatus for a secondary cell and a communications system. The deactivation method includes: restarting a deactivation timer associated with a first SCell carrying a PUCCH, in a case where a deactivation timer is restarted or a channel quality indicator report is transmitted in any second SCell in a secondary PUCCH cell group. Hence, a case will not occur where understanding of an activation state of a secondary cell by a UE and a base station is inconsistent due to an UE autonomous deactivation mechanism.