This study successfully obtained a chlorophyll-deficient mutant of Chlorella pyrenoidosa, named A19, using atmospheric and room temperature plasma mutagenesis technology. Compared to the wild-type strain, the A19 mutant exhibited a faster growth rate and appeared yellow under dark conditions. The content of chlorophyll A and chlorophyll B decreased by 80% and 60%, respectively, while lutein content increased by 16%. A19 also demonstrated improved amino acid quality. Transcriptome analysis revealed upregulation of gene expression levels in glycolysis and tricarboxylic acid cycle pathways, promoting central carbon flow towards enhanced production capacity and accelerating growth. Meanwhile, downregulation of genes regulating enzymes in the chlorophyll synthesis pathway explained the observed color change in the mutant strain. These results confirmed that A19 not only shifts its color to yellow but also exhibits faster growth, higher lutein content, and improved metabolic efficiency, making it a promising additive for feed and food applications while reducing cultivation time.