The invention relates to a fault diagnosis system sensor optimal configuration method based on a quantitative structure model. The method comprises the following steps: 1) establishing a structure model of a fault diagnosis system through a structure analysis method, wherein the structure model is represented by two matrixes, that is an analytical redundant relation matrix and a fault feature matrix, and the structure model can qualitatively describe the fault diagnosis system; 2) detecting nondeterminacy with the structure model of the fault diagnosis system and sensors being combined to obtain quantitative description of the fault diagnosis system and realize the purpose of quantitatively analyzing the fault diagnosis system, and establishing a calculation formula for fault diagnosis system key performance indicators with the detection of nondeterminacy being taken into consideration; 3) establishing a sensor optimization model of the fault diagnosis system; and 4) solving the optimization model through a genetic algorithm. The sensor optimal configuration method for the fault diagnosis system can effectively save the cost of the sensors of the fault diagnosis system, and the configuration result accords with engineering practice situations better.