In this study, we aimed to evaluate the fruit quality of Prunus humilis and identify cultivars that could provide superior human health benefits. We measured the basic characteristics, bioactive compounds, and antioxidant capacities of 137 P. humilis accessions. Flavonoid and phenol content were determined via colorimetry and ultrahigh performance liquid chromatography. Single fruit and stone weights varied widely and were genetically diverse among accessions. The variation in soluble solid content was comparatively narrow. Total flavonoid content (TFC) ranged from 3.90 to 28.37 mg/g FW, with an average of 10.58 mg/g FW in 2019. Significant differences between accessions in terms of TFC, total phenol content, and antioxidant capacity were found. TFC in the accessions was normally distributed and predominantly in the medium range (9.57-15.23 mg/g FW). Red was the predominant peel color over all other phenotypes (i.e., dark red, red, light red, red-orange, and yellow). There was no obvious correlation between peel color and TFC. Catechin was the major flavonoid component in the fruit. Principal component analysis showed that TFC, ABTS, single fruit weight, and vertical and horizontal diameter contributed to the first two principal components for each accession. Accessions 10-02, 3-17-2, 3-17-4, and JD1-6-7-37 were characterized by high TFC, ABTS, and large fruit. We believe that our results will aid in the breeding and functional food processing of Prunus humilis.