This　paper　aims　to　solve　the　problem　of　high　throughput　automated　data　analysis　of　brain　microstructure　reconstruction　by　using　the　solution　of　systems　engineering　that　consists　of　hardware,　software　and　algorithm.　To　solve　the　key　issues　of　limit　analysis　efficiency　such　as　registration　of　large-volume　distorted　image,　dense　neural　structure　recognition,　ambiguous　neural　connections　and　multi-source　data　fusion　etc,　classification　method　in　accordance　with　the　biological　characteristics　of　neural　structure　is　proposed　by　the　realization　of　the　samples　preparation,　automatic　cutting,　microscopic　imaging,　3D　reconstruction　and　software　platform　building　etc.　Furthermore,　it　provides　a　theoretical　basis　and　solution　for　building　engineering　platform　for　large　volume　neural　structure　reconstruction　and　meets　the　brain　science　research　of　high-throughput　neural　circuit　network　reconstruction　demand.　©　2017,　Editorial　Board　of　Journal　of　Systems　Engineering　Society　of　China.　All　right　reserved.