It is very easy to form bottom defects during friction stir welding (FSW) of medium-thick/thick Ti alloys, while there is a lack of in-depth research on its essential cause. In this study, conventional FSW (CFSW), dynamic rotation FSW (DRFSW) and back heating assisted FSW (BHAFSW) were conducted to 6mm Ti-6Al-4V plates. The combination of experimental examination and finite element modelling was utilized to deeply study the bottom defect formation mechanism. The results showed that bottom defects always existed in both CFSW and DRFSW joints, which was mainly attributed to the phase transformation difference at the joint bottom, as the result of the difference of the bottom temperature and the phase transformation point. A proper bottom temperature compensation of 150oC via BHAFSW was designed to avoid the phase transition difference and improve the material flow, which effectively eliminated the bottom defects. This is the first time to uncover the reason of the bottom defect generation during FSW, and thus defect-free Ti alloy medium-thick plate joints were achieved via BHAFSW. The BHAFSW joint achieved the 1022MPa in strength and 16% in ductility, with the equal strength to the base material (BM) but with very few losses of the ductility. The joint exhibited an impact toughness of 10.4J, 48.1% higher than the BM. This study uncovers the reason for the typical bottom defect and provides a new way to improve the quality of medium-thick/thick Ti alloy FSW joints.