As an effective nitrate removal process with lower sludge production, sulfur-based autotrophic denitrification (SAD) has attracted extensive attention in recent years. This study investigated a modified anaerobic baffled reactor coupled with a vibration frame (MV-ABR) for the SAD process to treat nitrate contaminated water. The nitrate removal rate (NRR) of 0.34 kg NO3−-N·m−3·d−1 was obtained under an ambient temperature. With adding oyster shells in two steps, the maximum NRR can be further increased from 0.34 kg NO3−-N·m−3·d−1 to 0.37 kg NO3−-N·m−3·d−1. The MV-ABR also achieved a strong impact resistance and robustness nitrogen removal performance under transient shocks. In addition, coupling the anaerobic baffled reactor (ABR) with the vibration method demonstrated that vibration could improve the denitrification performance, even under low temperatures (10 °C–15 °C). Under a suitable intermittent vibration intensity (level 1 (5–60)), the average NRR increased from 0.26 kg NO3−-N·m−3·d−1 to 0.35 kg NO3−-N·m−3·d−1, which suggests this is an economic and effective method for the SAD process. Overall, these results suggest that the MV-ABR could boost the SAD treatment performance, and present a stable nitrate removal performance even under a lower temperature environment (<15 °C) or transient shocks.