A general fault diagnosis method is proposed for modular dc-dc converter system. The magnetic component voltage in each module is chosen as diagnostic signal, which can be easily obtained by adding an auxiliary winding into each magnetic core. Based on the feature of these signals, two logical hardware circuits are designed to achieve fast fault detection for different demands. Fault can be detected within one switching period, which enables a fast reconfiguration for continuous operation. The input-series-output-parallel (ISOP) modular dc-dc system is analyzed as an example. Fault diagnosis principle, hardware implementation, reconfiguration, and experimental verification are given in this paper.