The profiling of disease-related biomarkers is an essential procedure for the accurate diagnosis and intervention of metabolic disorders. Therefore, the development of ultrasensitive and highly selective fluorogenic biosensors for diverse biomarkers is extremely desirable. There is still a considerable challenge to prepare nanocluster-based fluorescence turn-on probes capable of recognizing multiple biomolecules. We herein provide a novel nanocluster-based chemical information processing system (CIPS) for the programmable detection of various metabolites and enzymes. This CIPS consists of biocatalytic reactions between substrates and their respective oxidases to generate H2O2, which was then employed to synthesize bright fluorescent silver nanoclusters (Ag NCs). Utilizing this system, we are able to accurately probe a series of substrates/corresponding oxidases with high sensitivity and specificity, including glucose/glucose oxidase, uric acid/uric acid oxidase, sarcosine/sarcosine oxidase, choline/choline oxidase, xanthine/xanthine oxidase, and lactic acid/lactic acid oxidase. Furthermore, this metabolite profiling CIPS can be integrated with binary logic operations, which create an intelligent tool for the high-throughput screening of various diseases in vitro (e.g., diabetes, gout, prostate cancer, cardiovascular disease, and lactic acidosis).