Flutter is an aerodynamic instability on a long span bridge that can cause damage to the entire bridge deck structure. The interaction between wind and structure in long span bridges can be investigated by numerical simulation. In this study, an aeroelastic simulation was performed on a 2 DoFs sectional model of a long-span bridge deck with free vibration techniques to analyze flutter speed and determine the effect of deck shape on flutter instability characteristics using ANSYS software. The simulation result data was then extracted using the Modified Ibrahim Time-Domain Method (MITD) identification method to obtain the damping ratio and flutter derivatives coefficients. The damping ratio value is used to determine the critical flutter speed, whereas the coefficient flutter derivatives is used to determine the characteristics of flutter instability and the flutter mechanism that occurs in the bridge. The results showed that the rectangular shape (bluff body) is more susceptible to flutter instability than the streamlined shape, and has a lower flutter speed value than the other shapes. The flutter mechanism that occurs is torsional flutter, whereas in the streamline body is coupling flutter.