Based on a three-axis turntable, a whole performance assessment testbed of navigation system is designed and implementation. The testbed is mainly made up of the data acquisition and storage system, data comparison and analysis system and a turntable. The navigation system under test can be assembled on the turntable and move together with the standard navigation system. Then the whole performance can be analyzed by comparing the data from the system under test and standard system with the developed method. A famous open source flight controller Pixhawk is researched in our work. Based on the Pixhawk the navigation system performance with Extended Kalman Filer (EKF) and complementary filter algorithm are compared and analyzed, which verified the feasibility and validity of the system. In the future, more system and algorithm will be assessed for improving the application performance of the navigation system.