A method for handling Transmission Time Interval (TTI) bundle retransmission in a user equipment (UE) of a wireless communication system is disclosed. The UE operates in a TTI bundling mode. The method includes steps of performing a bundle retransmission of a TTI bundle, which is triggered by a Hybrid Automatic Retransmission Request (HARQ) process responsible for the TTI bundle, and determining whether to generate a non-adaptive retransmission for a current transmission opportunity according to a last received feedback of this HARQ process no matter whether the current transmission opportunity is a first transmission opportunity of the bundle retransmission when no uplink grant for the current transmission opportunity has been received on a Physical Downlink Control Channel (PDCCH).