Background:　Chlorella　sorokiniana　FZU60　is　a　promising　lutein　producing　microalga.　A　mixotrophy/photoautotrophy　two-stage　strategy　can　achieve　high　biomass　concentration　at　stage　1　and　high　lutein　content　at　stage　2,　leading　to　excellent　lutein　production　efficiency　in　C.　sorokiniana　FZU60.　However,　the　underlying　molecular　mechanisms　are　still　unclear,　restraining　the　further　improvement　of　lutein　production.　Results:　In　this　study,　physiological　and　biochemical　analysis　revealed　that　photochemical　parameters　(Fv/Fm　and　NPQ)　and　photosynthetic　pigments　contents　increased　during　the　shift　from　mixotrophy　to　photoautotrophy,　indicating　that　photosynthesis　and　photoprotection　enhanced.　Furthermore,　transcriptomic　analysis　revealed　that　the　glyoxylate　cycle　and　TCA　cycle　were　suppressed　after　the　shift　to　photoautotrophy,　leading　to　a　decreased　cell　growth　rate.　However,　the　gene　expression　levels　of　photosynthesis,　CO2　fixation,　autophagy,　and　lutein　biosynthesis　were　upregulated　at　the　photoautotrophy　stage,　demonstrating　that　microalgal　cells　could　obtain　more　precursor　to　synthesize　lutein　for　enhancing　photosynthesis　and　reducing　reactive　oxygen　species.　Conclusions:　The　findings　help　to　elucidate　the　molecular　mechanisms　for　high　lutein　production　efficiency　of　C.　sorokiniana　FZU60　under　the　mixotrophy/photoautotrophy　strategy,　identify　key　functional　genes　responsible　for　lutein　biosynthesis,　and　shed　light　on　further　improvement　of　lutein　production　by　genetic　or　metabolic　engineering　in　future　studies.　©　2023,　The　Author(s).