The coupled process of anammox and reduced-sulfur driven autotrophic denitrification can simultaneously remove nitrogen and sulfur from wastewater, while minimizing energy consumption and sludge production. However, the research on the coupled process for removing naturally toxic thiocyanate (SCN-) is limited. This work successfully established and operated a one-stage coupled system by co-cultivating mature anammox and SCN--driven autotrophic denitrification sludge in a single reactor. In this one-stage coupled system, the average total nitrogen removal efficiency was 89.68±3.33 %, surpassing that of solo anammox (81.80±2.10 %) and SCN--driven autotrophic denitrification (85.20±1.54 %). Moreover, the average removal efficiency of SCN- reached 99.50±3.64 %, exceeding that of solo SCN--driven autotrophic denitrification (98.80±0.65 %). The results of the 15N stable isotope tracer labeling experiment revealed the respective reaction rates of anammox and denitrification as 106.38±10.37 μmol/L/h and 69.07±8.07 μmol/L/h. By analyzing metagenomic sequencing data, Thiobacillus_denitrificans was identified as the primary contributor to SCN- degradation in this coupled system. Furthermore, based on the comprehensive analysis of nitrogen and sulfur metabolic pathways, as well as the genes associated with SCN- degradation, it can be inferred that the cyanate (CNO) pathway was responsible for SCN- degradation. This work provided a deeper insight into coupling anammox with SCN--driven autotrophic denitrification in a one-stage coupled system, thereby contributing to the development of an effective approach for wastewater treatment involving both SCN- and nitrogen.