A semiconductor structure and a manufacturing method thereof are provided. A semiconductor structure includes top, bottom, and middle tiers. The bottom tier includes a first interconnect structure overlying a first semiconductor substrate, and a first front-side bonding structure overlying the first interconnect structure. The middle tier interposed between and electrically coupled to the top and bottom tiers includes a second interconnect structure overlying a second semiconductor substrate, a second front-side bonding structure interposed between the top tier and the second interconnect structure, and a back-side bonding structure interposed between the second semiconductor substrate and the first front-side bonding structure. A bonding feature of the second front-side bonding structure includes a first bonding via in contact with the second interconnect structure, a first bonding contact overlying the first bonding via, and a barrier layer interface between a bottom of the first bonding contact and a top of the first bonding via.