Friction stir welding (FSW) was performed on thick plates of high-strength low-alloy (HSLA) steel with polycrystalline cubic boron nitride (PCBN) tools. To investigate the mechanism of microstructure formation in the stir zone (SZ), the prior austenite structure undergone through a thermo-mechanical history during the FSW process was investigated. The prior austenite structure was reconstructed by the local crystal orientations of prior austenite calculated from the bainite orientations by using the Kurdjumov–Sachs orientation relationship between the prior austenite and bainite. The reconstructed austenite revealed a heterogeneity in the SZ. The austenite grain size in the advancing side (AS) of SZ was larger than that of the retreating side (RS). Thus, a reheated temperature of AS was considered to be higher than that of RS. The textures of reconstructed austenite were also different in SZ. The rolling texture was observed in RS, but the shear texture was observed in the center and AS. The heterogeneous microstructure and texture in SZ was considered to be caused by the material flow behavior in FSW process.