Pogostemon oil (PO) is a volatile oil extracted from Pogostemon cablin., a traditional Chinese medicinal plants. Clinical studies have confirmed that PO has broad-spectrum antibacterial activity, but the resistance and protective mechanism of PO against Streptococcus agalactiae (SA) infection in Genetically Improved Cultured Tilapia (GIFT, Oreochromis niloticus.) are still unclear. The purpose of our study was to verify the resistance of PO feed to SA infection and reveal the potential immune mechanism. These 252 Tilapias were randomly divided into three groups, each with three replicates. The control group CON was fed with basic diet; These experimental groups PO5 and PO15 were fed with 5 μ L / g, 15 μ L / g PO diet, respectively; After 28 days feeding, Tilapia were randomly selected from CON, PO5, and PO15 groups, respectively: 22 fishes in each group were intraperitoneally injected with PBS to produce NC, NP5, and NP15 groups; other 22 fishes in each group were intraperitoneally injected with SA to produce CK, SP5, and SP15 groups. Twelve hours after SA challenge, spleen tissues were collected to study the effect of PO feed resist SA infection in Tilapia by RNA-Seq. In addition, two independent acute SA challenge experiments were added to verify the protective ability of PO against SA infection. In the transcriptome results, co-expressed genes in MEgreen (divided by WGCNA) were enriched in immune-related pathways by KEGG analysis, including Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway, MAPK signaling pathway, NOD-like receptor signaling pathway, and C-type lectin receptor signaling pathway. Cluster analysis of 166 shared DEGs responsible to SA infection identified two major clusters with almost opposite expression trends. il-1β (interleukin-1 beta), gpr84 (G protein-coupled receptor 84), and OXER1 (oxoeicosanoid receptor 1) belonged to both share DEGs and key co-expressed genes, were up-regulated by PO after SA infection. In the survival challenge of LD50 concentration of SA, 5μL / g (0.67% vs 53.33%, P < 0.01), 10 μL / g (0.67% vs 53.33%, P < 0.01), and 15 μL / g (33.33% vs 53.33%, P > 0.05) PO feed groups decreased Tilapia mortality compared to basic diet group. In the challenge of SA concentration 10 times higher than LD50, 15 μL / g PO feed (55% vs 95%, P < 0.05) reduced mortality compared to basic diet group, and 5 μL / g PO feed significantly prolonged the median survival time of 1 day. In general, 5–15 μL / g PO feeds improved the resistance of Tilapia to SA infection and reduced the mortality of Tilapia. The results of RNA-Seq provide data support for the molecular mechanism of PO feeds regulating the immune response of Tilapia to SA. Collectively, PO may have the potential to be developed as a dietary supplementation for preventing and treating SA infections.