Chlorella　sorokiniana　is　a　promising　candidate　for　lutein　production.　However,　the　diversified　pigment　composition　results　in　a　complex　and　costly　extraction　process.　In　this　study,　a　chlorophyll-deficient　mutant　(MT03)　of　C.　sorokiniana　FZU60　was　generated　by　chemical　mutagenesis,　exhibiting　lutein　as　the　primary　pigment　under　heterotrophic　conditions　with　higher　content　and　production　than　the　wild　type　(WT).　Transcriptomic　and　biochemical　composition　analyses　showed　the　decreased　contents　of　carbohydrates,　lipids,　and　chlorophylls　in　MT03,　which　might　lead　to　the　increased　biosynthesis　of　lutein　and　protein.　The　inhibition　of　chlorophyll　biosynthesis　also　triggered　the　enhanced　heme　biosynthesis,　potentially　promoting　the　functions　of　cytochrome　P450　carotenoid　hydroxylases　and　subsequently　facilitating　lutein　biosynthesis　in　MT03.　Sequencing　analysis　indicated　that　the　mutation　of　G1106　to　D1106　in　MT03　CHLH　might　hinder　the　magnesium　chelating　reaction,　leading　to　the　deficiency　in　chlorophyll　biosynthesis.　These　findings　highlight　the　potential　of　MT03　as　a　promising　strain　for　lutein-directed　biosynthesis　and　provide　a　straightforward　and　cost-effective　approach　for　enhancing　microalgae-based　lutein　production.