Chinese cherry is an economically significant fruiting cherry species within Rosaceae family. Soluble sugar and organic acid are crucial factors affecting fruit flavor, while the genetic basis for these traits in Chinese cherry remains largely unknown. In this study, we determined sugar and acid components in 190 and 187 representative hybrids from an intraspecific cross of Chinese cherry over two consecutive years. Fructose and glucose were the major sugars in both progeny and parents, but their contents varied considerably between years. Fructose represented a higher proportion in progeny than in parents. Malic acid was the most predominant component, accounting for a relatively stable proportion (∼70%) for both years. The F1 population exhibited wide phenotypic variations, with coefficient of variation ranging from 6.57% to 108.63%. Regarding inheritance patterns, sugars tended towards smaller values, while malic acid exhibited significant transgressive heterosis. Sugars and acids were primarily governed by 2 MG-AD or 2 MG-EA model. Major gene heritability exceeded 88% for acids but much lower (12%–75%) for sugars. These results suggest that acid contents might be controlled by two major genes, while sugars are mainly governed by polygenes. This study provides a theoretic basis for understanding genetic predisposition underlying sugar-acid fractions in Chinese cherry fruit.