Cerasus humilis fruit is known for its high acidity, surpassing that of most other fruits. The metabolism of organic acids in these fruits significantly influences sugar and calcium accumulation. However, research on this metabolic process is limited. This study investigates the organic acid metabolism and the accumulation patterns of sugars and calcium during the development of Cerasus humilis fruits. Using low−acid and high−acid varieties from Inner Mongolia, we compared organic acid components and the activity of relevant metabolic enzymes during fruit maturation. We also measured the content and proportions of various sugars and calcium forms, performing correlation analyses. Throughout the development and ripening of Cerasus humilis fruits, organic acids, sugars, and calcium exhibited consistent patterns of change across the two acidity types. Malic acid emerged as the most significant organic acid, while fructose was the primary sugar, and active calcium was the dominant calcium component. Correlation analyses indicated that malic acid and total acid positively correlated with sugar and water−soluble calcium content, negatively regulating other calcium forms. Conversely, NADP−ME, citric acid, and oxalic acid negatively correlated with sugars and water−soluble calcium, while positively affecting other calcium forms. In conclusion, the metabolism of organic acids during the development and maturation of Cerasus humilis fruits is closely linked to the accumulation of sugars and calcium. Malic acid, primarily regulated by NAD−MDH and NADP−ME, promotes the accumulation of sugars and water−soluble calcium but inhibits other calcium forms, while citric and oxalic acids inhibit sugar accumulation and promote non−water−soluble calcium forms.