This study conducted friction stir welding (FSW) by using the butt welding process to join ferritic ductile iron plates and investigated the variations of microsturcture in the joined region formed after welding. No defects appeared in the resulting experimental weld, which was formed using a 3-mm thick ductile iron plate and tungsten carbide alloy stir rod to conduct FSW at a rotational speed of 982rpm and traveling speed of 72mm/min. The welding region was composed of deformed graphite, martensite phase, and dynamically recrystallized ferrite structures. In the surface region and on the advancing side (AS), the graphite displayed a striped configuration and the ferritic matrix transformed into martensite. On the retreating side (RS), the graphite surrounded by martensite remained as individual granules and the matrix primarily comprised dynamically recrystallized ferrite. After welding, diffusion increased the carbon content of the austenite around the deformed graphite nodules, which transformed into martensite during the subsequent cooling process. A micro Vickers hardness test showed that the maximum hardness value of the martensite structures in the weld was approximately 800HV. An analysis using an electron probe X-ray microanalyzer (EPMA) indicated that its carbon content was approximately 0.7–1.4%. The peak temperature on the RS, 8mm from the center of the weld, measured 630°C by the thermocouple. Overall, increased severity of plastic deformation and process temperature near the upper stir zone (SZ) resulted in distinct phase transformation. Furthermore, the degree of plastic deformation on the AS was significantly greater than that on the RS, and relatively complete graphite granules and the fine ferrite grains resulting from dynamic recrystallization were observed on the RS.