Signal-in-space range error (SISRE) has direct impact on the performance of global navigation satellite system (GNSS). It is an important indicator of navigation satellite space server performance. Compared to the BeiDou Regional Navigation Satellite System (BDS-2) satellites, Beidou Global Navigation Satellite System (BDS-3) satellites are equipped with new hydrogen atomic clock and new rubidium atomic clock. The accuracy and stability of the new hydrogen and rubidium clocks on BDS-3 satellites need annual analysis of long time series, which will affect the service quality of this system. Based on precise ephemeris products from Center for Orbit Determination in Europe (COD), the orbit error, clock error and SISRE of 24 medium earth orbit (MEO) satellites’ D1 navigation message of BDS-3 is computed, analyzed and compared. Thanks to the use of inter-satellite links (ISLs) adopted by BDS-3 MEO satellites, the percent of ages of data, ephemerides (AODEs) and ages of data, clocks (AODCs) shorter than 12 hours are 99.95% and 99.96%, respectively. In the same way, the broadcast ephemeris orbit performance is also improved by the ISLs. The root mean square (RMS) values of BDS-3 MEO broadcast ephemeris orbit error are 0.067 m, 0.273 m and 0.297 m in radial, cross and along direction, respectively. And the 3D RMS value of the orbit error can reach up 0.450 m. With respect to clock errors, the timescale differences between the broadcast ephemeris and precise ephemeris are eliminated to assess the accuracy to broadcast ephemeris clock error. The standard deviation value of 0.256 m shows a good performance as a result of the use of the two new types atomic clocks, but the RMS value is 0.541 m due to a nonzero mean bias. For the new hydrogen and rubidium atomic clocks, their RMS and standard deviation are 0.563 m, 0.231 m and 0.519 m, 0.281 m respectively. The stability of the hydrogen atomic clock is better than that of the rubidium atomic clock. However, the accuracy of rubidium atomic clock is better than that of hydrogen atomic clock. The RMS value of SISRE of BDS-3 MEO satellites’ D1 navigation message is 0.556 m, and the RMS value is 0.920 m when it with 95% confidence level. While after deducting the influence of the clock error, the RMS value of orbit only SISRE (SISRE_ORB) is 0.092 m. Because the SISRE_ORB is mainly affected by orbit radial error, its accuracy is high and stable throughout the year. Since the satellite clock error is much larger than orbit radial error, the SISRE is mainly affected by the clock error.