A fault protecting method of an independent micro-grid is based on a short-time energy segment and can be used for accurately determining whether a fault of the micro-grid occurs. Fault current information is used for realizing fault positioning based on fault detection. The fault current and the short-time energy segment are used as fault determining criteria. Misoperation of an independent micro-grid protecting device because of outer interference and abrupt load change is prevented. The short-time energy segment (SES) is a characteristic quantity which reflects energy flow magnitude on a line and represents magnitude of the energy which flows on the line in a power frequency period T. Whether the fault of the independent micro-grid occurs is determined through comparing current effective values and short-time energy segments of an early period and a late period. The fault protecting method can be adapted with topological structure change of the micro-grid and realizes adaptive adjustment of a protecting setting value. The current effective value and SES of a period before the fault are used as the setting criteria for determining whether the fault of the independent micro-grid occurs.