As important silkworm varieties reared on artificial diet, Youshi No. 1 (YS) and Guangshi No. 1 (GS) showed remarkable differences in physiological characteristics. GS had significantly better performance than YS in body weight, cocooning ability, food intake, feed utilization efficiency, and digestive enzyme activities. We further performed metabolomics and 16S rRNA high-throughput sequencing to analyze their metabolic profiles and midgut microbiota. More than 40 differential metabolites were screened out, and four metabolic pathways related to feeding divergence were determined via KEGG enrichment, among which L-valine was enriched in multiple pathways. Significant structural differences were also observed in midgut microbiota, and Bacillus was positively correlated with pantothenic acid and valine metabolism. These correlational results disclosed that differential metabolites and gut microbiota might underlie the phenotypic variations between the two varieties. Integrated analysis combined with functional verification experiments demonstrated that supplementation of 1% L-valine or specific Bacillus strains in an artificial diet was associated with the improvement of the growth performance, cocoon quality, and feed utilization efficiency of the YS silkworm variety.