The structural evolution of Typhoon Morakot (2009) during its passage across Taiwan was investigated with the WRF model. When Morakot approached eastern Taiwan, the low-level center was gradually filled by the Central Mountain Range (CMR), while the outer wind had flowed around the northern tip of the CMR and met the southwesterly monsoon to result in a strong confluent flow over the southern Taiwan Strait. When the confluent flow was blocked by the southern CMR, a secondary center (SC) without a warm core formed over southwestern Taiwan. During the northward movement of the SC along the west slope of the CMR, the warm air produced within the wake flow over the northwestern CMR was continuously advected into the SC, contributing to the generation of a warm core inside the SC. Consequently, a well-defined SC with a warm core, closed circulation and almost symmetric structure was produced over central western Taiwan, and then it coupled with Morakot’s mid-level center after crossing the CMR to reestablish a new and vertically stacked typhoon. Therefore, the SC inside Morakot was initially generated by a dynamic interaction among the TC’s cyclonic wind, southwesterly wind and orographic effects of the CMR, while the thermodynamic process associated with the downslope adiabatic warming effect documented by previous studies supported its development to be a well-defined SC. In summary, the evolution of the SC in this study is not in contradiction with previous studies, but just a complement, especially in the initial formation stage.