Cucumber (Cucumis sativus L.) is a major vegetable crop worldwide, and its yield and quality are closely linked to flower development. AGAMOUS-LIKE 6 (AGL6), a member of the ancient MADS-box transcription factor family, plays a crucial role in flower development. However, the specific functions of its homolog in cucumber remain poorly understood. In this study, we demonstrate that CsAGL6 is predominantly expressed in flowers, with high expression levels observed in all floral organ primordia during the early stages of floral development. The petals of Csagl6 mutants exhibit a greener color compared to wild-type plants, along with a significant increase in total chlorophyll content. Additionally, the mutants show abnormal petal morphology, including changes in size and shape, as well as enlarged sepals resembling leaves occasionally. Molecular analysis reveals that CAULIFLOWER (CAL) and the E-class gene SEPALLATA 4 (SEP4) are significantly downregulated in the mutants, while the chlorophyll synthesis gene Early Light-Induced Protein 1 (ELIP1) and several stress-related genes in the chloroplasts are dramatically upregulated. Our findings provide novel insights into the functional role of CsAGL6 in regulating sepal and petal development, and offer a potential avenue for understanding the genetic control of flower pigmentation and organ morphology in Cucumis species.