Appearance of smart distribution system makes protection technology face new challenges, a feeder protection algorithm based on graph theory for smart distribution system is proposed. Using graph theory, analyzing directed graph of distribution network, dividing all IEDs into interconnected group and reserve interconnected group, the fault section can be diagnosed and isolated through fault overcurrents information from IED, the principle is simple and less information is required. Impacts of such abnormal conditions as misfunction of IED or circuit breaker and the change of network topology are discussed. To cope with abnormal conditions the fault-tolerance algorithms are given. The result of case show that the fault estimation results are exact and immune against abnormal conditions.