Meretrix petechialis is a commercial marine mollusk widely cultivated along the coastal areas of China, renowned for its delicious flavor. Its rich umami is primarily determined by free amino acids. Among the umami-related amino acids detected in the foot tissue of 300 two-year-old individuals, alanine was identified as the most abundant [(0.351±0.092) g/100 g wet weight] and genetically variable component, making it a key target trait for improving the flavor characteristics. The present study integrated multiple omics approaches, including genome-wide association study (GWAS), expression-based GWAS (eGWAS), transcriptome-wide association study (TWAS), and weighted gene co-expression network analysis (WGCNA) , to decipher the genetic architecture and regulatory network governing alanine content. GWAS, based on 9.8 million high-quality SNPs, identified four significantly associated loci on chromosomes 2, 4, 16, and 17, which explained 8.35% to 9.10% of the phenotypic variation. These loci were annotated to two core candidate genes: PRSS48,which is a serine protease potentially regulates alanine accumulation by promoting protein hydrolysis and precursor supply, and FUT11, which is a fucosyltransferase inferred to modulate the activity and stability of alanine metabolic enzyme through glycosylation. Colocalization analysis between GWAS and eGWAS revealed a highly credible shared causal variant at chr17:23364804 (PP.H4=1.000), which overlaps with a cis-eQTL signal of the downstream gene evm_TU_Hic_asm_16_887, indicating cis-regulatory control of gene expression in alanine metabolism. Using transcriptomic data from 100 randomly selected individuals, TWAS identified 30 alanine-correlated genes enriched in signal transduction, metabolic regulation, and post-translational modification pathways. WGCNA further delineated three functionally specialized modules significantly correlated with alanine content: the magenta module (enriched in amino acid metabolism and mTOR signaling), the red module (focused on glycolysis and branched-chain amino acid degradation), and the green module (involved in lysosomal function and detoxification), collectively orchestrating alanine synthesis, storage, and homeostasis. These multi-omics results comprehensively reveal the hierarchical regulatory mechanisms underlying the formation of umami amino acids in M. petechialis, integrating genetic variation, transcriptional regulation, and co-expression networks, providing valuable candidate genes and molecular markers for flavor-oriented molecular breeding in this commercial important shellfish.