On the basis of fault diagnosis neural network model, in this paper, knowledge representation system of rough set theory is taken as a major tool to delaminate the complex neural network and in which unnecessary properties are eliminated. This method overcomes some shortcomings, such as network scale is too large and the rate of classification is slow. The good effect that reduces the matching quantity of pattern search in classification course is gotten. The structure and algorithm of layered-mining neural network model based on rough set theory are also given. The example shows that this system has higher reference value in practical application.