Being the first hybrid-constellation global navigation system, China’s BeiDou navigation satellite system (BDS) has been entirely constructed since July 2020 and provides open services for worldwide users. Due to the natural sensitivity of satellite tracking techniques to geocenter motion, BDS has the capability to determine the geocenter coordinates independently. This study aims to improve the precision of geocenter coordinates derived from BDS. To that end, 3-year sets of daily geocenter coordinates have been determined with BDS observations. Different solar radiation pressure models, including the empirical CODE orbit model (ECOM), the extended ECOM model (ECOM2), and the adjustable box-wing (ABW) model, have been applied for the BDS geocenter estimation. We show that the ABW model appears to mitigate the draconitic signal of BDS and reduces the amplitude of the annual signal by factors of 5.4 and 2.1 w.r.t. ECOM and ECOM2 cases. Furthermore, we studied the impact of BDS constellation configuration on the geocenter estimation. The results indicate that the inclusion of IGSO satellites significantly mitigates the spurious signals in the spectra of the geocenter coordinates, with amplitudes of the annual signal and 3-cpy signal reduced by (28%, 14%), (33%, 61%), and (65%, 45%) for ECOM, ECOM2, and ABW cases, respectively. Meanwhile, the amplitude of the 7-day signal related to the revolution period of MEO satellites is also reduced by 43–60% after the inclusion of IGSO satellites. Thus, the MEO + IGSO hybrid configuration and ABW model are recommended for BDS to determine the geocenter. The annual amplitudes of the derived geocenter coordinates are 1.3, 3.6, and 5.5 mm, compared to 3.7, 3.2, and 5.0 mm for the ILRS solution in the X, Y, and Z components, respectively. Particularly, in the Z component, the BDS constellation characteristics lead to a difference of 15 mm in the amplitude of the 3-cpy signal compared to the ILRS solution.