Computational fluid dynamics (CFD) is one of the most important high performance computing (HPC) areas. CFD applications commonly access large volumes of data. In case of large-scale CFD parallel computing, serial I/O performance does not match the computing performance, hence it becomes the performance bottleneck. Parallel I/O is an effective way to solve this problem. HDF5 (hierarchical data format v5) has provided excellent mechanisms to manage scientific data as well as effective ways to implement parallel I/O. High-order simulator for aerodynamics (HOSTA) is a multi-zone structured grids CFD application that can solve real world flow problems. This paper implements the parallel I/O method in HOSTA, based on the HDF5 file format and corresponding parallel I/O application programming interface. Detailed performance evaluation is performed with real CFD simulation cases on a HPC system equipped with 6 I/O service nodes. The results show that our method is both scalable and efficient. For a delta wing test case, parallel I/O achieves the performance speedup of 21.27 compared with the serial I/O. It achieves maximal I/O throughput of 5.81GBps and improves the application’s performance by over 10%, as compared with the original code. For a simple airfoil test case with larger grid size, our parallel I/O achieves maximal I/O throughput of 6.72GBps.