According to experimental sectional flutter derivatives, indicial functions are used to simulate the self-excited loads of a bridge deck section, and their recursive formulas that are essential in the implementation of FE analysis procedure are given. The procedure of time-domain flutter analysis, which is achieved by APDL language, is performed by the ANSYS software. Numerical results show that geometric nonlinearities have a negligible effect on the flutter threshold, but show a significant effect on the post-flutter properties. When geometric nonlinearities are included, the post-flutter ultimately leads to a limit cycle oscillation (LCO) with very small amplitude compared with a formidable divergence resulted from a linear method. Furthermore, the analysis results show that, in the case of linear analysis, the energy stored in the structure increases continuously as time progresses. However, this energy is limited in a quite low level (LCO state) when geometric nonlinearities are involved. Compared with the traditional divergence and catastrophic collapses, LCO results in significant cumulative damage. In view of this, other factors, such as the material strength and fatigue properties, are indispensable for further evaluation of the security and stability of bridge structures.