FaSTAR developed by JAXA is a leading edge CFD (Computational Fluid Dynamics) program package which supports various solvers based on unstructured grids. The computation based on unstructured grid causes a lot of pipeline stalls by RAW (Read After Write) hazard when reconfigurable accelerators are implemented in FPGAs. In order to cope with this problem, the OoO (Out-of-Order) mechanism generator is proposed. By setting parameters depending on the target computation, the OoO mechanism with appropriate structure of the execution unit and waiting buffer is generated. The OoO mechanisms are applied to five subroutines in FaSTAR, and it achieved 2.6 times performance as the case of in-order execution, and 2.9 times as the software executed by Intel Core2Duo processor with reasonable amount of overhead.