An industrial-scale high throughput wafer bonding apparatus includes a wafer bonder chamber extending along a main axis and comprising a plurality of chamber zones, a plurality of heater/isolator plates, a guide rod system extending along the main axis, a pair of parallel track rods extending along the main axis, and first pressure means. The chamber zones are separated from each other and thermally isolated from each other by the heater/isolator plates. The heater/isolator plates are oriented perpendicular to the main axis, are movably supported and guided by the guide rod system and are configured to move along the direction of the main axis. Each of the chamber zones is dimensioned to accommodate an aligned wafer pair and the wafer pairs are configured to be supported by the parallel track rods. The first pressure means is configured to apply a first force perpendicular to a first end heater/isolator plate. The applied first force causes the heater/isolator plates to move toward each other along the main axis and thereby causes the collapse of each chamber zone volume and the application of bonding pressure onto the wafer pairs.