Fast Aerodynamics Routines (FaSTAR) is one of the most recent fluid dynamics software package. The problem of FaSTAR is hard to be executed in parallel machines because of its irregular and unpredictable data structure. Exploiting reconfigurable hardware with their advantages to make up for the inadequacy of the existing high performance computers had gradually become the solutions. However, a single FPGA is not enough for the FaSTAR package because the whole module is very large. Instead of using many FPGAs, partially reconfigurable hardware available in recent FPGAs is explored for this application. Advection term computation module in FaSTAR is chosen as a target subroutine. We proposed a reconfigurable flux calculation scheme using partial reconfiguration technique to save hardware resources to fit in a single FPGA. We developed flux computational module and five flux calculation schemes are implemented as reconfigurable modules. This implementation has advantages of up to 62.75% resource saving and enhancing the configuration speed by 6.28 times. Performance evaluation also shows that 2.65 times acceleration is achieved compared to Intel Core 2 Duo at 2.4 GHz.