A simple, high-accuracy and non-destructive method for the measurement of diaphragm thickness and microgap width based on modulated tri-beam interference is demonstrated. With this method, a theoretical estimation error less than 0.5% for a diaphragm thickness of ~1 μm is achievable. Several fiber-tip air bubbles with different diaphragm thicknesses (6.25, 5.0, 2.5 and 1.25 μm) were fabricated to verify our proposed measurement method. Furthermore, an improved technique was introduced by immersing the measured object into a liquid environment to simplify a four-beam interference into tri-beam one. By applying this improved technique, the diaphragm thickness of a fabricated in-fiber rectangular air bubble is measured to be about 1.47 μm, and the averaged microgap width of a standard silica capillary is measured to be about 10.07 μm, giving a corresponding measurement error only 1.27% compared with actual scanning electron microscope (SEM) results.