Femtosecond laser direct writing of glass waveguides is an important means to rapidly prepare three-dimensional integrated photonic chips, and the accurate measurement of the effective refractive index of waveguides is significant for designing photonic devices. A breaking-arm Mach-Zendel interferometer (MZI) structure is designed and fabricated for in-situ precise measurement of the effective refractive index of glass waveguides. The different effective refractive index of the laser in the breaking region and within the waveguide produces a certain phase difference at the same length of transmission, which eventually leads to different interference results. The phase interference results of the MZI of the breaking arm are processed to obtain the effective refractive index of the laser direct-written glass waveguide as 1.504+7.7×10^-4. The device is simulated by using the beam propagation algorithm of RSOFT, and the simulation results are in good agreement with the experimental results. This accurate measurement of the effective refractive index of the glass waveguide is of great significance for the enhancement of photonic chip design and fabrication.