The bonding performance between fiber reinforced polymer (FRP) rebar and concrete is one of the critical issues that affect the structural performance of FRP reinforced concrete elements. Self-compacting concrete (SCC) has been demonstrated as an alternative material to native to enhance the bonding with FRP rebar with refined interfacial transition zone (ITZ) between FRP rebar and matrix. Owing to the different material morphology, the bonding mechanism between FRP rebar and SCC could be different from that of normal concrete, which has not been understood comprehensively. In this study, the bonding performance between FRP rebar and SCC is investigated through direct pull-out tests coupled with acoustic emission techniques. The AE signal strength exhibited a good correlation with the bond-slip relationship measured in each specimen. Based on the AE location technique, the invisible non-uniform distribution of bonding stress along the bar was further revealed. Moreover, the mesoscale finite element analysis (FEA) has been conducted to illustrate the damage initiation and development between FRP rebar and SCC. The contribution of chemical adhesion, friction, and mechanical interlocking toward the bonding performance between FRP rebar and concrete is revealed through acoustic emission analysis and FEA. The findings from current study provide fundamental understanding on the bonding mechanism between FRP and concrete materials, which can be further adopted in the material design of FRP reinforced concrete structures for better bonding performance.