Beidou satellite navigation system error mainly include the error related to satellite, the error in signal transmission process and the error of user segment, which can cause the satellite navigation system cannot effectively warn of the positioning accuracy timely, alert limit appear obvious error, and even the positioning results cannot be used and integrity failure. According to the specification of the space signal interface, the analytical expression of satellite orbit error, satellite clock error, ionospheric error, troposphere error and user equivalent range error are derived by using broadcast ephemeris, precise ephemeris, original navigation message and pseudo-range. Then, based on the measured data near the airport received by Propak6 receiver, the errors of the Beidou navigation system are statistically analyzed, which can provide an important reference for Beidou navigation system applied to the field of civil aviation.