A method of manufacturing a semiconductor structure includes the following steps: providing a first semiconductor wafer, wherein the first semiconductor wafer includes a first dielectric layer and at least one first top metallization structure embedded in the first dielectric layer, and a top surface of the first dielectric layer is higher than a top surface of the first top metallization structure by a first distance; providing a second semiconductor wafer, wherein the second semiconductor wafer includes a second dielectric layer and at least one second top metallization structure embedded in the second dielectric layer, and a top surface of the second top metallization structure is higher than a top surface second dielectric layer of the by a second distance; and hybrid-bonding the first semiconductor wafer and the second semiconductor wafer.