Development of sensitive, accurate yet simplified fluorescence sensor array is crucial for rapid, multi-bacterial, on-site sensing applications. A fluorescence sensor array based on a multiplexing fluorescence probe (MFP, excitations/emissions with 278 nm/558 nm, 290 nm/364 nm, 362 nm/592 and 616 nm) was constructed. The positive MFP equipped with rich quinoline and pyridine groups can combine with the negative charge groups and electron-rich groups of bacterial surfaces, which causes the symbolic signal response in the sensing channels (four emissions and three excitations). The sensor array displayed sensitive response to bacteria even at a lower level (102 cfu mL−1) and high identification accuracy (100%) for drug-resistant bacteria, inactivated bacteria, and blends of bacteria. Furthermore, the developed sensor array demonstrated a high-throughput bacterial identification (92.1% accuracy) in real samples (pork and milk) with high sensitivity, rapid response, easy-to-operate, and independence of specific recognition elements, which would brighten the development of fluorescence sensor array.