The characteristics of the improved Atomic Frequency Standard (AFS) operated on the latest BeiDou-3 experimental satellites are analyzed from day-of-year (DOY) 254 to 281, of the year 2017, considering the following three aspects: stability, periodicity, and prediction precision. The two-step method of Precise Orbit Determination (POD) is used to obtain the precise clock offsets. We presented the stability of such new clocks and studied the influence of the uneven distribution of the ground stations on the stability performance of the clock. The results show that the orbit influence on the Medium Earth Orbit (MEO) clock offsets is the largest of three satellite types, especially from 3 x 10(3) s to 8.64 x 10(4) s. Considering this orbit influence, the analysis shows that the Passive Hydrogen Maser (PHM) clock carried on C32 is approximately 2.6 x 10(-14) at an interval of 10(4), and has the best stability for any averaging intervals among the BeiDou satellite clocks, which currently achieves a level comparable to that of the PHM clock of Galileo, and the rubidium (Rb) clocks of Global Positioning System (GPS) Block IIF. The stability of the improved Rb AFS on BeiDou-3 is also superior to that of BeiDou-2 from 3 x 10(2) s to 3 x 10(3) s, and comparable to that of Rb AFS on the Galileo. Moreover, the periodicity of the PHM clock and the improved Rb clock are presented. For the PHM clock, the amplitudes are obviously reduced, while the new Rb clocks did not show a visible improvement, which will need further analysis in the future. As expected, the precision of the short-term clock prediction is improved because of the better characteristics of AFS. The Root Mean Square (RMS) of 1-h clock prediction is less than 0.16 ns.