Based on the basic principle of upper wind sounding, a smoothing algorithm of upper wind used in routine operation for satellite navigation radiosonde system is presented. Firstly, the original upper wind is calculated in a geocentric coordinate system based on the second geodetic coordinate data provided by the Beidou-GPS dual-mode radiosonde. Then, the vector average method is adopted to smooth the original upper wind. Through comparative analysis with the RS92 radiosonde system launched on the same ball, the upper wind of the satellite navigation radiosonde system coincides with the RS92 radiosonde system under the condition that the moving average window is set to 34 s in the range of 0 to 32 km and 60 s above 32 km. The calculation result of this algorithm is basically the same as the 30 s moving average wind calculated in the local Cartesian coordinates coordinate system. However, its wind components’ confidence interval is slightly better below 32 km and obviously reduced above 32 km, and the error of the whole flight is more stable.