A novel variegated tea cultivar exhibiting a stable variegated phenotype was recently identified, demonstrating significantly elevated amino acid content concomitantly with reduced polyphenolic compound levels compared to conventional green-leaf varieties. Nevertheless, the underlying mechanism remains unclear. Here, variegated leaves and normal leaves of ‘Huangshanzhong’ tea plant were used to perform pigment content analysis and comparative transcriptome analysis. The chlorophyll content in variegated leaves significantly decreased compared to normal leaves, while the ratio of Chl a to Chl b was enhanced. Multiple genes (CsrpiA, CsGAPDH, CsPGAM, CsPK and CsOGDH) involved in sugar metabolism exhibited downregulated expression in variegated leaves. Key genes involved in the photosynthetic pathway were down-regulated in variegated leaves, including those encoding light-harvesting protein complex chlorophyll a/b binding proteins (CsLhca1, CsLhca4, CsLhcb1 and CsLhcb3) and photosystem II complex proteins (CspsbP and CspsbW). Meanwhile, genes involved in chlorophyll degradation metabolism (CsSGR and CsCLH1) were upregulated in variegated leaves. Compared to the wild type, transgenic plants overexpressing CsCLH1 and CsCLH2 exhibited no significant changes in chlorophyll content. Enzyme activity assays showed that CsCLH1 could degrade chlorophyll in vitro. Subcellular localization results revealed that CsCLH1 and CsCLH2 were localized in the cytoplasm and nucleus. These findings suggest that impaired photosynthetic system function, suppressed carbohydrate synthesis, and accelerated degradation of photosynthetic pigments collectively contribute to the variegated phenotype in tea leaves. This study advances our understanding of mechanisms underlying leaf variegation in plants.