As a solid state technology, friction stir welding (FSW) has been used to join titanium alloys for avoiding the fusion welding defects. So far, many previous studies have attempted to elucidate the microstructure characteristics and evolution during the FSW process of titanium alloy, but few are about the mechanism of microstructure transformation along the thickness direction of joint. For solving this problem, in this work, 2 mm thick TC4 titanium alloy is successfully welded by FSW. On the basis of numerical simulation, the effects of temperature distribution on the microstructure along the weld thickness direction and the tensile strength of welding joint were investigated. The results show that the peak temperatures of material close to weld surface exceed b phase transus temperature under the rotational speed of 300 r/min and the welding speed of 50 mm/min. With the increase of distance away from the weld surface, the peak temperature decreases. The peak temperature of weld bottom near the backing board is difficult to be higher than b phase transus temperature owing to quick heat radiation. The region, where the peak temperature is higher than b phase transus temperature, consists of primary a, lath-shape a and residual b phases. The size of lath-shape a inside the weld is larger than that near the weld surface. Primary a and b phases with smaller size are attained in the weld bottom owing to the dynamic recrystallization, and the distribution of b phase on primary a matrix is more homogeneous. When the rotational speed reaches 350 r/min, the area where the peak temperature is higher than b phase transus temperature becomes wider along the thickness direction, which makes the size and quantity of lath-shape a phase increase and then the lath-shape a clump appears. Lath-shape a phase with different orientations hinder the propagation of crack and be beneficial for the tensile strength of FSW joint.