The invention relates to a micro-grid protection method. The method comprises the steps: a total current I and a system frequency f of a micro-grid line are sampled in real time; a total harmonic current I is calculated; within a time range of [T, T+deltaT], when the total harmonic current I on the micro-grid line sharply rises and a system frequency change, namely an absolute value of f<2>-f<1>, of the micro-grid exceeds a preset deviation setting valve f, the condition that the micro-grid line is in a short circuit at the moment of T+deltaT is judged; and a micro-grid protection is started, wherein T is an arbitrary sampling moment; deltaT is not lower than 1/F; F is the sampling frequency; f<1> is the system frequency at the moment T; f<2> is the system frequency at the moment T+deltaT; and the value range of the f is 2Hz to 3Hz. According to the micro-grid protection method, the sharp rise quantity of a harmonic component in the short circuit current is adopted as a criterion and a frequency deviation value is adopted as an auxiliary criterion, so that a relay protection of the micro-grid can be accurately achieved.