To　research　the　operation　mechanism　of　brain　for　realizing　brain-inspired　intelligence,　we　employ　the　deep　learning　tool　system　to　solve　the　problems　of　automatic　analysis　of　big　data　in　synaptic-scale　brain　microstructure　reconstruction.　The　problems　include　dense　neurons　reconstruction,　single　neuron　tracing,　key　organelles　detection　and　reconstruction.　Meanwhile,　we　adopt　the　fully　convolutional　networks　(FCN)　with　a　candidate　region　proposal　network　(RPN)　to　detect　mitochondria　and　synapses,　and　integrate　deep　SPPUnet　(spatial　pyramid　pooling　U-net)　framework　with　multi-cut　algorithm　for　neurons　reconstruction.　Preferable　performance　have　achieved　in　visual　and　quantitative　analysis.　These　works　provide　effective　support　for　high-throughput　synaptic-scale　brain　microstructure　reconstruction　for　neuroscientists.　©　2018,　Editorial　Board　of　Journal　of　Systems　Engineering　Society　of　China.　All　right　reserved.