Cerasus humilis (Bge) Sok (C. humilis) is a perennial wild fruit tree endemic to China. Its fruits are rich in phenolics and organic acids and have high nutritional and exploitation value. The coordinated developmental changes in the organic acid-phenolic compound-antioxidant system are central to the formation of fruit functional quality. However, germplasm-specific differences in this coordinated regulatory network throughout the entire fruit developmental cycle remain poorly understood in C. humilis germplasm with distinct phenolic levels. In this study, two superior C. humilis lines with similar genetic backgrounds - the low-phenolic line MY-23 and the high-phenolic line MY-25 - were used as experimental materials. The main aim was to systematically analyze the dynamic physiological and biochemical patterns during fruit development and ripening. We quantified six organic acid fractions, the activities of key enzymes involved in malate metabolism, the contents of four phenolic compounds, the activities of four antioxidant enzymes, and four comprehensive antioxidant capacity indicators across five consecutive developmental stages from the young fruit stage to the full ripening stage. Combined with Pearson correlation analysis and principal component analysis (PCA), we characterized the different coordinated developmental patterns of the organic acid-phenolic compound-antioxidant system between low- and high-phenolic C. humilis fruits. Malic acid dominated the organic acid profile. At full ripeness, high-phenolic fruits maintained higher NAD-MDH activity and had numerically higher malic acid and total acid contents (17.89% and 10.26%, respectively); however, the difference in malic acid between lines was not significant after Holm-Bonferroni adjustment. The two lines showed contrasting developmental patterns in phenolic classes. In both lines, anthocyanins accumulated while total phenols, total flavonoids, and proanthocyanidins declined. However, the high-phenolic line retained markedly higher levels of total phenols, total flavonoids, and proanthocyanidins during the late stages. Antioxidant capacity declined during ripening, but it was markedly higher in high-phenolic fruits during the late ripening stages, especially at full ripeness, and the primary active substances differed. This work documents the systematic differences among organic acids, phenolics, and antioxidants, and provides a physiological reference for germplasm selection and quality improvement of C. humilis.