Two methods are widely used for evaluating the precision of satellite clock products, namely the single-satellite method (SSM) and the multi-satellite method (MSM). In the satellite clock product evaluation, an important issue is how to eliminate the timescale difference. The SSM selects a reference satellite to eliminate the timescale difference by between-satellite differencing, but its evaluation results are susceptible to the gross errors in the referenced satellite clock offsets. In the MSM, the timescale difference is first estimated and then removed. Unlike the GPS, the BeiDou Navigation Satellite System (BDS) consists of three types of satellites, namely geosynchronous earth orbit (GEO), inclined geosynchronous orbit (IGSO), and medium earth orbit (MEO) satellites. The three types of satellites have uneven orbital accuracy. In the generation of satellite clock products, the orbital errors are partly assimilated into the clock offsets. If neglecting the orbital accuracy difference of the three types of BeiDou satellites, the MSM will obtain biased estimates of the timescale difference and finally affect the clock product evaluation. In this study, an improved multi-satellite method (IMSM) is proposed for evaluating the real-time BDS clock products by removing the assimilated orbital errors of the three types of BDS satellites when estimating the timescale difference. Three real-time BDS clock products disseminated by three different International GNSS Service (IGS) analysis centers, namely CLK16, CLK20, and CLK93, over a period of two months are used to validate this method. The results indicate that the assimilated orbital errors have a significant impact on the estimation of the timescale difference. Subsequently, the IMSM is compared with the SSM in which the referenced satellite is rigorously chosen, and their RMS difference is only 0.08 ns, which suggests that the evaluation results obtained by the IMSM are accurate. Compared with the traditional MSM, the IMSM improves the RMS by 0.16, 0.11, and 0.07 ns for CLK16, CLK20, and CLK93, respectively. Finally, three real-time BDS clock products are evaluated using the proposed method, and results reveal a significant precision difference among them.