A three-dimensional (3D) numerical study of bubble formation process in viscous fluids in a microfluidic flow-focusing junction is carried out in the present study. The numerical approach is first validated by the experimental data and shows a very good agreement, and a reciprocal relationship can be derived between the normalized bubble length and liquid fraction. Afterwards, the numerical approach is further applied to study bubble formation in fluids with different viscosities ranging from 5.6 to 400 mPa s, and the viscosity ratio of liquid phase to gas phase (μl/μg) is up to 2.2 × 104. Two different interpolation treatments including the Geo-Reconstruction method and the CICSAM are implemented when dealing with the situation for high viscosity, and the results are compared with the experimental data, indicating a better performance of the Geo-Reconstruction method. The numerical results of the bubble shapes are also compared with the experimental visualization results, showing good agreements. The evolution of the gas tip is further investigated quantitatively, and the liquid film is found to play a very important role in affecting the velocity of the gas tip. Finally, the hydrodynamic behaviors of the Taylor bubble formed in the junction including velocity and pressure distributions are studied in detail, and the contribution of pressure drop within the channel is also discussed.