Microorganisms have high application value in the field of drug development such as antibacterial and anti-tumor. By using genetic engineering to modify microorganisms, intelligent engineering bacteria can be contained that can sense, transmit, compute, and feedback disease signals in real time. In this review, three crucial aspects in the construction of intelligent engineering bacteria were summarized, including the selection of chassis strains, the construction of a biosensor system, and the design of a controlled release mode of functional factors. The clinical applications of intelligent engineering bacteria in the adjunctive diagnosis and treatment of metabolic diseases, inflammatory diseases, tumors, and infectious diseases were further discussed. The challenges and prospects of the current research were also analyzed to provide reference for relevant personnel.