Pink-flowered Prunus sibirica, of the genus Prunus, is an exceptional germplasm resource with high ornamental value. Understanding the mechanism behind petal coloration is crucial for cultivating ornamental P. sibirica varieties. This study utilized pink-flowered and white-flowered P. sibirica petals at different stages of flowering to explore the relationship between various physiological indicators, anatomical structures of petals, and flower coloration during flowering. Results indicated that anthocyanins, key pigment indicators in pink-flowered P. sibirica, directly influenced the a* values (redness). Increased activity of phenylalanine deaminase (4.43-29.69 U/g), chalcone isomerase (9.80-46.67 U/g), and soluble sugar content (29.25-35.28 mg/g) promoted anthocyanin synthesis and accumulation. These substances indirectly affected flower color by influencing anthocyanin content through physiological processes related to petal coloration. Structural changes in epidermal cells of pink and white flower petals during flowering were similar, with differences in pigment content and distribution impacting petal light absorption. Correlation analysis revealed that a* values were significantly and positively correlated with five factors, one of which was anthocyanin content, and significant negative correlations with soluble protein content and cytosol pH. This study examined the factors influencing petal coloration in pink-flowered P. sibirica from both physiological and anatomical perspectives, providing a theoretical foundation for breeding new varieties of ornamental flowering plants.