In the present work, we report a novel colorimetric sensor array for rapid identification of heavy metal ions. The sensing mechanism is based on the competition between thiols and urease for binding with the metal ions. Due to the different metal ion-binding abilities between the thiols and urea, different percentages of urease are free of metal ions and become catalytically active in the presence of varied metal ions. The metal ion-free urease catalyzes the decomposition of urea releasing ammonia and changing the pH of the analyte solution. Bromothymol blue, the pH indicator, changes its color in response to the metal-caused pH change. Three different thiols (l-glutathione reduced, l-cysteine, and 2-mercaptoethanol) were used in our sensor array, leading to a unique colormetric repsonse pattern for each metal. Linear discriminant analysis (LDA) was employed to analyze the patterns and generate a clustering map for identifying 11 species of metal ions (Ni2+, Mn2+, Zn2+, Ag+, Cd2+, Fe3+, Hg2+, Cu2+, Sn4+, Co2+, and Pb2+) at 10 nM level in real samples. The method realizes the simple, fast (within 30 s), sensitive, and visual discrimination of metal ions, showing the potential applications in environmental monitoring.