Leaf color mutants are important materials for studying chloroplast and photomorphogenesis, and can function as basic germplasms for genetic breeding. In an ethylmethanesulfonate mutagenesis population of watermelon cultivar “703”, a chlorophyll-deficient mutant with yellow leaf (Yl2) color was identified. The contents of chlorophyll a, chlorophyll b, and carotenoids inYl2leaves were lower than those in wild-type (WT) leaves. The chloroplast ultrastructure in the leaves revealed that the chloroplasts inYl2were degraded. The numbers of chloroplasts and thylakoids in theYl2mutant were lower, resulting in lower photosynthetic parameters. Transcriptomic analysis identified 1292 differentially expressed genes, including1002 upregulated and 290 downregulated genes. The genes involved in chlorophyll biosynthesis (HEMA,HEMD, CHL1,CHLM, andCAO) were significantly downregulated in theYl2mutant, which may explain why chlorophyll pigment content was lower than that in the WT. Chlorophyll metabolism genes such asPDS,ZDSandVDE, were upregulated, which form the xanthophyll cycle and may protect the yellow‒leaves plants from photodamage. Taken together, our findings provide insight into the molecular mechanisms of leading to leaf color formation and chloroplast development in watermelon.