In this paper, a three-dimensional (3D) finite element model was established by ABAQUS software to simulate the welding temperature field of a Ti-6Al-4V alloy under different welding currents based on a Gaussian heat source model. The model uses thermo-mechanical coupling analysis and takes into account the effects of convection and radiation on all weld surfaces. The microstructure evolution of the molten pool was calculated using the macro-micro coupling cellular automaton-finite different (CA-FD) method. It was found that with the increase of the welding current, the temperature in the central region of the moving heat source was improved and the weld bead became wider. Then, the dendritic morphology and solute concentration of the columnar to equiaxed transition (CET) in the weld molten pool was investigated. It is shown that fine equiaxed crystals formed around the columnar crystals tips during solidification. The coarse columnar crystals are produced with priority in the molten pool and their growth direction is in line with the direction of the negative temperature gradient. The effectiveness of the model was verified by gas tungsten arc welding experiments.