Objective To explore the short-term effect of rare earth yttrium on anaerobic ammonia oxidation system and reveal its short-term mechanism of action. Method We measured the nitrogen removal performance and anaerobic ammonium oxidation activity (SAA) of the anaerobic ammonium oxidation system at different yttrium concentrations (0, 1, 2, 4, 10, 20, 40, and 100 mg/L), conducted a significance analysis of SAA using Origin software, and determined the sludge characteristics and key enzyme activities of the anaerobic ammonium oxidation system at varying yttrium concentrations using scanning electron microscopy-energy dispersive spectroscopy, three-dimensional fluorescence spectroscopy, Fourier transform infrared spectroscopy, Coomassie brilliant blue method, phenol sulfuric acid method and the double-antibody sandwich method. Result When the yttrium concentration is 2 mg/L, the total nitrogen removal rate of the system is the highest, which is 1.98% higher than the control group. Continuing to increase the concentration of yttrium, the total nitrogen removal rate of the system gradually decreases. Low concentration yttrium enhances anaerobic SAA, promotes the secretion of extracellular polymers and the synthesis of cytochrome C, increases the proportion of C, N, P, and Fe elements on the surface of granular sludge, promotes the generation of soluble microbial metabolic byproducts and humic acid substances in TB-EPS, increases the intensity of functional group characteristic peaks related to heavy metal adsorption, and enhances the activity of hydrazine synthase, nitrate reductase, and nitrite reductase. However, high concentrations of yttrium have the opposite effect, while significantly increasing the proportions of phosphorus and yttrium. Yttrium adhered to the granular sludge surface in crystalline form, further promoting the secretion of extracellular polymeric substances, moreover the activities of hydrazine synthase, nitrate reductase, and nitrite reductase remained relatively high. However, the spatial structures of enzymes were disrupted and overall metabolic function was impaired. Conclusion Rare earth yttrium has a short-term “promotion at low concentration and inhibition at high concentration” effect on anaerobic ammonia oxidation systems.