The invention discloses a method and system for simulating electromagnetic transient states of micro grids in real time. According to the method and system, a blocking and layering parallel manner is utilized to realize the precision and efficiency of simulating the electromagnetic transient states of the micro grids; the parallel manner comprises blocking and equivalence of a network and layering and solution of sub-networks; the blocking and equivalence of the network comprises blocking and equivalence, wherein the blocking part indicates determining sizes and port input variables of basic sub-networks, and the equivalence part indicates determining differencing state variable equations and external characteristic equations of the basic sub-networks; and the layering and solution of the sub-networks comprises combination of the sub-networks and reverse deduction of port inputs: combining the adjacent sub-networks into combined sub-networks of a higher layer, obtaining external characteristic equations and reverse deduction equations of the combined sub-networks, reversely deducing port inputs of the lower-layer sub-networks via the port inputs of the combined sub-networks, obtaining the port inputs of all the basic sub-networks and determining state variables of the basic sub-networks.