Microalgae　can　accumulate　various　compounds　simultaneously,　thus　co-production　of　high-value　metabolites　to　improve　the　economic　value　of　microalgae　production　is　feasible.　In　this　study,　a　microalga　strain　Nitzschia　sp.　FZU62　capable　of　co-producing　fucoxanthin　and　eicosapentaenoic　acid　(EPA)　was　isolated　and　identified.　Further,　heterotrophic　conditions　were　optimized　to　improve　the　co-production　efficiency　in　flasks.　Results　showed　that　the　optimal　conditions　for　flask　culture　were　cultivation　for　84　h　with　an　inoculum　size　of　0.47　g/L　and　a　temperature　of　19　°C.　Besides,　three　fed-batch　culture　strategies　with　distinct　nutrient　compositions　were　explored　to　improve　the　heterotrophic　performance　of　strain　FZU62.　Results　indicated　that　the　highest　biomass,　fucoxanthin,　and　EPA　productivities　were　obtained　by　Fed-batch　III,　in　which　concentrated　medium　was　pulse-fed　to　supply　60　%　initial　nutrients　once　glucose　concentration　dropped　to　about　2　g/L.　Moreover,　the　heterotrophic　performance　was　verified　in　a　5　L　fermenter,　resulting　in　excellent　fucoxanthin　and　EPA　productions　of　63.03　and　398.60　mg/L,　and　productivities　of　3.41　and　22.52　mg/L/d,　respectively.　These　results,　especially　the　EPA　production　and　productivity,　are　superior　to　many　literature　reports.　The　present　study　provides　new　insights　into　the　highly　efficient　co-production　of　fucoxanthin　and　EPA　by　marine　microalgae　and　has　guiding　significance　for　commercial　production　in　heterotrophic　mode.　©　2023　Elsevier　B.V.