Global Navigation Satellite System (GNSS) carrier phase measurement for short baseline meets the requirements of deformation monitoring of large structures. However, the carrier phase multipath effect is the main error source with double difference (DD) processing. There are lots of methods to deal with the multipath errors of Global Position System (GPS) carrier phase data. The BeiDou navigation satellite System (BDS) multipath mitigation is still a research hotspot because the unique constellation design of BDS makes it different to mitigate multipath effects compared to GPS. Multipath error periodically repeats for its strong correlation to geometry of satellites, reflective surface and antenna which is also repetitive. We analyzed the characteristics of orbital periods of BDS satellites which are consistent with multipath repeat periods of corresponding satellites. The results show that the orbital periods and multipath periods for BDS geostationary earth orbit (GEO) and inclined geosynchronous orbit (IGSO) satellites are about one day but the periods of MEO satellites are about seven days. The Kalman filter (KF) and Rauch-Tung-Striebel Smoother (RTSS) was introduced to extract the multipath models from single difference (SD) residuals with traditional sidereal filter (SF). Wavelet filter and Empirical mode decomposition (EMD) were also used to mitigate multipath effects. The experimental results show that the three filters methods all have obvious effect on improvement of baseline accuracy and the performance of KT-RTSS method is slightly better than that of wavelet filter and EMD filter. The baseline vector accuracy on east, north and up (E, N, U) components with KF-RTSS method were improved by 62.8%, 63.6%, 62.5% on day of year 280 and 57.3%, 53.4%, 55.9% on day of year 281, respectively.