The paper describes the application of Multilevel Flow Modeling (MFM)-a modeling method in means-end and part-whole way, in interfacs design of supervisory control of Pressurized Water Reactor (PWR) plant, and automatic real-time fault diagnosis of PWR accident. The MFM decomposes the complex plant process from the main goal to each component at multiple levels to represent the contribution of each component to the whole system to make clear how the main goal of the system is achieved. The plant process is described abstractly in function level by mass, energy and information flows, which represent the interaction between different components and enable the causal reasoning between functions according to the flow properties. Thus, in the abnormal status, a goal-function-component oriented fault diagnosis can be performed with the model at a very quick speed and abnormal alarms can be fully explained by the reasoning relationship of the model. In this paper, an interfacs design of the PWR plant is built by the conception of means-end and part-whole by using MFM, and several simulation cases are used for evaluating the fault diagnosis performance. The results show that the system has a good ability to detect and diagnose accidents timely before reactor trip.