The performance analysis and evaluation of satellite navigation systems under ionospheric scintillation have been a focal point in the field of modern aviation. With the development and upgrading of satellite navigation systems, the performance indicators and evaluation techniques of these systems also require continuous iteration and optimization. In this study, based on the ionospheric scintillation model and satellite navigation algorithm, we designed a software tool to evaluate the performance of GNSS aviation services under various ionospheric scintillation intensities. The software is implemented in the C/C++ programming language and provides assessment capabilities for different ionospheric scintillation environments and flight phases. By encapsulating the software task modules using technologies such as dynamic link libraries and thread pools, the software can flexibly adjust the ionospheric scintillation intensity and control the flight trajectory. This ensures the strong scalability and reusability of the software. The software supports the performance evaluation of aviation services during all flight phases of global flights and is compatible with GPS, BDS, GALILEO, and GLONASS systems. Through verification of the accuracy, integrity, continuity, and availability of the GNSS system under different flight phases and ionospheric scintillation effects, the effectiveness of the software design has been validated.