Ultra-high finesse micro-resonator plays an important role in realizing the interaction between atoms and cavity field in the study of cavity quantum electrodynamics (QED) system, weak optical nonlinear effects and micro-optic devices. By measuring basic parameters of the microcavity, the atom-cavity coupling coefficient and the cavity decay rate can be determined precisely. It is also useful for exploring the dynamic characteristics of the system. However, it has difficulty in determining resonate frequency and effective cavity length due to the structure of the ultra-high finesse optical microcavity itself and the characteristics of multilayer coating. In this paper, we demonstrate the precision measurement of effective cavity length under different resonant frequencies which our cavity mirror is coated with 37 layers of dielectric film. The theoretical expectation when using the revised model of the multilayer coating agrees well with that of the experiment; and the measurement error for longitudinal mode interval is below 0.004 nm which is two orders of magnitude better than that obtained in previous unrevised model. The tiny depths into mirror coatings that the standing-wave light field inside the cavity penetrates are given for different mode numbers. This method may be applied to other micro resonator in the precision measurement.