According　to　C4ISR　architecture,　the　configuration　method　for　the　complex　large-scale　system　is　introduced.　The　C4ISR　system　mainly　contains　four　sub-systems　which　are　information　perception　system,　electronic　antagonizing　system,　command　and　control　system,　and　network　communication　system.　The　performance　models　of　the　sub-systems　are　set　up,　and　the　layered　configuration　model　based　on　multi-objective　genetic　algorithm　(MOGA)　is　constructed.　Each　system　is　configured　reasonably　through　model　solutions.　Finally,　the　simulation　experiment　is　designed　to　have　proved　that　the　proposed　method　is　effective　and　feasible,　and　it　also　can　provide　reference　and　basis　for　application.