Provided is a hybrid bonding apparatus including a plurality of chambers, and a transferer configured to transfer a plurality of wafers between the plurality of chambers and transfer a plurality of bonded wafers to an annealing chamber, the plurality of wafers including a plurality of substrate wafers and a plurality of die supply wafers, wherein the plurality of chambers respectively includes a wafer supplier configured to store the plurality of wafers, a bonding device configured to bond the plurality of wafers, the bonding device including a bonder configured to bond dies on the plurality of substrate wafers from the plurality of die supply wafers, and a pre-annealing oven configured to primarily anneal the plurality of substrate wafers, and a processor.