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<i>Chlamydomonas reinhardtii</i> is a unicellular green alga that can grow heterotrophically by using acetate as a carbon source. Carotenoids are natural pigments with biological activity and color, which have functions such as antioxidant, anti-inflammatory, vision protection, etc., and have high commercial value and prospects. We transformed <i>Chlamydomonas reinhardtii</i> with the <i>BKT</i> genes from <i>Phaffia rhodozyma</i> (<i>PrBKT</i>) and Chlamydomonas reinhardtii (<i>CrBKT</i>) via plasmid vector, and screened out the stable transformed algal strains C18 and P1. Under the condition that the cell density of growth was not affected, the total carotenoid content of C18 and P1 was 2.13-fold and 2.20-fold higher than that of the WT, respectively. <i>CrBKT</i> increased the levels of β-carotene and astaxanthin by 1.84-fold and 1.21-fold, respectively, while <i>PrBKT</i> increased them by 1.11-fold and 1.27-fold, respectively. Transcriptome and metabolome analysis of C18 and P1 showed that the overexpression of <i>CrBKT</i> only up-regulated the transcription level of <i>BKT</i> and <i>LCYE</i> (the gene of lycopene e-cyclase). However, in P1, overexpression of <i>PrBKT</i> also led to the up-regulation of <i>ZDS</i> (the gene of ζ-carotene desaturase) and <i>CHYB</i> (the gene of β-carotene hydroxylase). Metabolome results showed that the relative content of canthaxanthin, an intermediate metabolite of astaxanthin synthesis in C18 and P1, decreased. The overall results indicate that there is a structural difference between <i>CrBKT</i> and <i>PrBKT</i>, and overexpression of <i>PrBKT</i> in <i>Chlamydomonas reinhardtii</i> seems to cause more genes in carotenoid pathway metabolism to be up-regulated.