While sulfur-driven autotrophic denitrification (SDAD) occurring in the anoxic reactor of the sulfate reduction, autotrophic denitrification and nitrification integrated (SANI) system has been regarded as the main nitrogen removal bioprocess, little is known about the accompanying Anammox bacteria whose presence is made possible by the co-existence of NH4+ and NO2-. Therefore, this work firstly developed an integrated SDAD-Anammox model to describe the interactions between sulfur-oxidizing bacteria and Anammox bacteria. The model was subsequently used to explore the impacts of influent conditions on the reactor performance and microbial community structure of the anoxic reactor. The results revealed that at a relatively low ratio of <1.5 mg S/mg N, Anammox bacteria could survive and even take a dominant position (up to 58.9%). Finally, a modified SANI system configuration based on the effective collaboration between SDAD and Anammox processes was proposed to improve the efficiency of the treatment of sulfate-rich saline sewage.