Having　known　the　3D　structures　of　chromosomos　is　of　great　importance　to　the　understanding　of　gene　expression　and　regulation　in　nuclei.　Hi-C　technology　has　been　developed　to　capture　genome-wide　interactions　and　generate　contact　frequency　data.　Based　on　the　characteristic　of　the　sparse　and　noisy　interaction　sampling　in　Hi-C　data,　a　MBO-based　method　with　parameter　optimization,　named　VMBO,　was　proposed　to　predict　a　3D　chromatin　structure.　First,　for　converting　the　interaction　frequency　to　spatial　distance　between　two　chromosome　fragments　the　conversion　factor　was　optimized　by　golden　section　search.　Second,　manifold　based　optimization　(MBO)　was　applied　to　reconstruct　a　consensus　3D　structure.　The　VMBO　accuracy　and　robustness　were　validated　on　both　simulation　data　and　real　Hi-C　data.　The　results　of　structure　similarity　measures,　root　mean　squared　deviation　and　distance　Spearman　correlation　coefficient,　indicate　that　the　proposed　method　can　well　reconstruct　3D　chromatin　structures.　©　2018,　Editorial　Department　of　Journal　of　Beijing　University　of　Technology.　All　right　reserved.