The qualitative and quantitative analysis of anions is a big challenge to current optical sensing techniques. In this work, we report a colorimetric sensor array for discrimination of twenty-nine anions by applying silver and gold nanoparticles as nanozymes. This array was composed of silver and gold nanoparticles stabilized with different organic capping agents with catalytic activity which were able to accelerate the oxidation reaction of 3,3′,5,5′-tetramethylbenzidine (TMB) in the presence of H2O2. The obtained results were shown that the catalytic activity of nanozymes was inhibited or activated by introducing anions into array, resulting in providing different colorimetric responses and fingerprint-like patterns for each anion. Then, standard statistical methods such as principal component analysis (PCA) and hierarchical clustering analysis (HCA) were used to analyze the obtained patterns and generate a clustering map for classifying 29 anions at four concentration levels of 5.0, 7.5, 10.0, and 12.5 mg L−1. The proposed array was also provided a linear detection range from 2.5 to 12.5 and 0.5 to 7.5 mg L−1 for cyanide and sulfide, respectively.