In this study, a novel method to assemble a micro-accelerometer by a flip chip bonding technique is proposed and demonstrated. Both the main two parts of the accelerometer, a double-ended tuning fork and a base-proof mass structure, are fabricated using a quartz wet etching process on Z cut quartz wafers with a thickness of 100 μm and 300 μm, respectively. The finite element method is used to simulate the vibration mode and optimize the sensing element structure. Taking advantage of self-alignment function of the flip chip bonding process, the two parts were precisely bonded at the desired joint position via AuSn solder. Experimental demonstrations were performed on a maximum scale of 4 × 8 mm² chip, and high sensitivity up to 9.55 Hz/g with a DETF resonator and a Q value of 5000 in air was achieved.