The　endoplasmic　reticulum　(ER)　is　a　contiguous　and　complicated　membrane　network　in　eukaryotic　cells,　and　membrane　contact　sites　(MCSs)　between　the　ER　and　other　organelles　perform　vital　cellular　functions,　including　lipid　homeostasis,　metabolite　exchange,　calcium　level　regulation,　and　organelle　division.　Here,　we　establish　a　whole　pipeline　to　reconstruct　all　ER,　mitochondria,　lipid　droplets,　lysosomes,　peroxisomes,　and　nuclei　by　automated　tape-collecting　ultramicrotome　scanning　electron　microscopy　(ATUM-SEM)　and　deep　learning　techniques,　which　generates　an　unprecedented　3D　model　for　mapping　liver　samples.　Furthermore,　the　morphology　of　various　organelles　and　the　MCSs　between　the　ER　and　other　organelles　are　systematically　analyzed.　We　found　that　the　ER　presents　with　predominantly　flat　cisternae　and　is　knitted　tightly　all　throughout　the　intracellular　space　and　around　other　organelles.　In　addition,　the　ER　has　a　smaller　volume-to-membrane　surface　area　ratio　than　other　organelles,　which　suggests　that　the　ER　could　be　more　suited　for　functions　that　require　a　large　membrane　surface　area.　Our　data　also　indicate　that　ER‒mitochondria　contacts　are　particularly　abundant,　especially　for　branched　mitochondria.　Our　study　provides　3D　reconstructions　of　various　organelles　in　liver　samples　together　with　important　fundamental　information　for　biochemical　and　functional　studies　in　the　liver.