In this study, short-term batch experiment was used to investigate the mechanism of thiocyanate (0~500mg/L) addition on the anammox granular sludge system. The results showed that as the concentration of thiocyanate influent increased, nitrogen removal efficiency of Anammox decreased significantly, and the total nitrogen removal efficiency decreased from 88.6% in the control group to 43.3% (500mg/L thiocyanate); The anammox activity (SAA) also showed a rapid decreasing trend. The non-competitive inhibition model determined the 50% inhibitory concentration (IC₅₀) of thiocyanate on Anammox to be 209.5mg/L. The EPS secreted by Anammox cells increased after the addition of thiocyanate. The PN/PS increased with the rise of the concentration of thiocyanate. The relative abundance of Candidatus Brocadia was significantly decreased after the addition of thiocyanate, while the relative abundance of Thiobacillus increased sharply, and The abundance of microbial functional metabolism pathways appeared to be reduced to different degrees. The research results can provide a theoretical basis for the application of Anammox engineering in treating nitrogenous wastewater containing thiocyanate.