A bonding apparatus includes a wafer stage, a first chip stage, a first chip transporting device, a second stage and a second chip transporting device. The wafer stage is used for holding a wafer. The first chip stage is used for holding at least one first chip. The first chip transporting device is used for transporting the first chip from the first chip stage onto the wafer. The second chip stage is used for holding at least one second chip. The second chip transporting device is used for transporting the second chip from the second chip stage onto the wafer.