Echinacea purpurea extract, a traditional herbal food additive with dual-purpose of medicine and edible material, has been widely used for the treatment and prevention of various infectious diseases, especially for children, old aged and immunocompromised patients. Although there were numerous reports suggested E. purpurea possessed immunostimulatory and antibacterial effects in vitro, the mechanisms underlying remained to be elucidated. This study employed immunologic factors analysis, GC-TOFMS based metabolomics and 16S-rRNA-sequencing microbiome profiling technologies to explore the effects of E. purpurea on young rats, a physiological insufficient immunity status, by compared with pidotimod treatment on young rats and adult animals. E. purpurea treatment significantly increased IL-2, decreased IL-6 and affect immunoglobulins in the spleen of young rats, indicating its promotion of cellular immunity. Both the immunologic factors and the global metabolome of E. purpurea treated young rats were close to the status of mature individuals. Results of 16S-rRNA-sequencing of ileum content together with co-metabolism metabolites demonstrated that E. purpurea changed gut microbiota structure characteristically as a reducing Firmicutes phylum, especially Lactobacillus, and a rising Actinobacteria phylum including Bifidobacterium. The results were concluded that E. purpurea could potentially promote the maturation of immune and metabolism of immature rats, and also affect gut flora structure.