Understanding the dynamics and thermodynamics of Artic cyclones is significant in revealing the insights of the continually increasing Arctic cyclones in recent decades. In this research, we conducted an experiment with the Weather Research and Forecast model (WRF) model that simulates an intensive cyclone system in August 2016. The cyclone originated in the north of the Barents Sea and then intensified when propagating eastward along the Eurasian shelf seas. It also experienced a merging process with a prior cyclone system located near the center of the Arctic Ocean on Aug 14th. A noticeable transition of its two-stage dynamic structures is observed approximately before and after the merge of the two cyclones: the new system pre-merge shows strong baroclinicity, while the post-merge system is dominated by a barotropic structure. Dynamic diagnostic analysis indicates that a large value of the maximum Eady Growth Rate (EGR) occur through all pressure levels pre-merge but decreases vastly after merge. The cyclone exhibits a cold core from the lower to upper troposphere and warm core in the lower stratosphere, which result from coupling processes between the cyclone system and the downward intrusion of a potential vorticity (PV) anomaly. The similar structures was also discovered in a cyclone system observed in September 2010. The vertical differential of vorticity advection and Laplacian of temperature advection in the isobaric Omega equation contributes differently to the cyclone development, as measured by the vertical motion, between the two stages. The dynamic structures and mechanisms revealed in this study further distinguish the Arctic cyclone system from a conventional mid-latitude, baroclinic-instability-dominant cyclones.