The hybrid integration of multiple chips in three dimensions is an important technology for realizing highly functional, compact optoelectronic microsystems. In this study, three-dimensional integration of optical chips was successfully performed using Au-Au surface-activated bonding (bonding temperature: 150 °C). The fabricated microsystem consists of two elements: i) a micromachined silicon optical bench incorporating a bonded laser diode, micromirrors, and through-hole electrodes; and ii) a glass substrate incorporating bonded photodiodes, electrical interconnections, and refractive microlenses. The silicon optical bench and the glass substrate were vertically stacked by surface-activated bonding. The size of the fully integrated microsystem is only 2.6 mm × 2.6 mm × 1 mm thick. The design and fabrication process allow chip-scale and wafer-level packaging. In addition, application for laser Doppler velocimeter sensor is discussed.