Purple pearls, which are exclusively produced by the freshwater pearl mussel, Hyriopsis cumingii (Lea, 1852), are of great economic and ornamental value. Selection mussels with purple inner shell as donor mussel can realize oriented cultivation of purple pearls. This study sought to explore the genomic genetic parameters of inner shell color traits as well as genomic-based methods to improve inner shell purpleness using genomic selection (GS). Genotype by sequencing (GBS) technology was used to generate genome-wide SNPs (n = 97,090) for reference population (n = 496) and candidate population (n = 268). In reference population, the four inner shell color phenotypes, lightness (L*), redness (a*), yellowness (b*), and color difference (dE*) were 59.97 ± 7.27, 2.66 ± 2.57, 1.79 ± 4.77, and 40.65 ± 7.46, respectively, and the genomic heritability of four traits were moderately high (0.39–0.67). GBLUP and four Bayesian models were applied to assess the prediction accuracy, where BayesB performed the best and it was chosen to develop a cost-effective GS method using low-density SNPs. Lastly, one GS method that consisted of BayesB model and 5 K GWAS-informative SNPs was successfully established and the genomic estimated breeding value (GEBV) of each candidate individual was predicted. The mussels with the highest GEBVs (n = 30) were selected as broodstocks for breeding the purple strain (PS), while the rest for control strain (CS). Significant differences in inner shell color a* and dE* were detected between PS and CS, as well as the proportion of deep purple individuals rose from 9.57% and 12.38% to 51.16% and 26.92% in Wuyi (WY) and Chongming (CM) sites, respectively. These results demonstrated that GS was an effective selective breeding approach for enhancing the purpleness of the inner shell in H. cumingii, and opened the door for future commercial GS uses on other aquaculture species.