Microfabrication technology with quartz crystals is gaining importance as the miniaturization of quartz MEMS devices is essential to ensure the development of portable and wearable electronics. However, until now, there have been no reports of dimension compensation for quartz device fabrication. Therefore, this paper studied the wet etching process of Z-cut quartz crystal substrates for making deep trench patterns using Au/Cr metal hard masks and proposed the first quartz fabrication dimension compensation strategy. The size effect of various sizes of hard mask patterns on the undercut developed in wet etching was experimentally investigated. Quartz wafers masked with initial vias ranging from 3 μm to 80 μm in width were etched in a buffered oxide etch solution (BOE, HF:NH4F = 3:2) at 80 °C for prolonged etching (>95 min). It was found that a larger hard mask width resulted in a smaller undercut, and a 30 μm difference in hard mask width would result in a 17.2% increase in undercut. In particular, the undercuts were mainly formed in the first 5 min of etching with a relatively high etching rate of 0.7 μm/min (max). Then, the etching rate decreased rapidly to 27%. Furthermore, based on the etching width compensation and etching position compensation, new solutions were proposed for quartz crystal device fabrication. And these two kinds of compensation solutions were used in the fabrication of an ultra-small quartz crystal tuning fork with a resonant frequency of 32.768 kHz. With these approaches, the actual etched size of critical parts of the device only deviated from the designed size by 0.7%. And the pattern position symmetry of the secondary lithography etching process was improved by 96.3% compared to the uncompensated one. It demonstrated significant potential for improving the fabrication accuracy of quartz crystal devices.