Macrophage is an essential part of the native immune system, however, Streptococcus agalactiae has the ability to survive in macrophage in order to get into the central nervous system. To learn about the interaction of S. agalactiae and macrophage, we go through this study which can lay the foundation for further analysis of the intracellular survival mechanism of S. agalactiae in macrophages. In this study, we investigated the genome-wide transcriptional changes of S. agalactiae after phagocytosis by RAW264.7 and explored the metabolic pathways and genes associated with the intracellular survival of S. agalactiae. S. agalactiae strain HN016 was co-incubated with RAW264.7 and the intracellular bacteria were subjected to transcriptome sequencing (RNA-seq), Gene Ontology (GO), and KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis. HN016 was incubated with primary macrophages of tilapia in vitro and RNA of intracellular bacteria were extracted. Quantitative Real-time PCR (qPCR) was used to verify the expression of the target genes. The results showed that a total of 1215 differentially expressed genes (DEGs), including 869 up-regulated genes and 319 down-regulated genes, were screened compared to the untreated group. DEGs significantly enriched in all three of the Molecular function, Biological process, and Cellular component in the GO enrichment. The KEGG enrichment results showed that the major enrichment pathways were the ABC transporter, ribosome, population sensing, and glycolysis/gluconeogenesis pathways. In the DEGs, 27 virulence-associated genes were screened, including fbsA (+8.65), sip (+6.28), cylD (+4.93), and cfb (-4.65). qPCR was used to validate the RNA-seq results and the agreement between the two data proved that the results of RNA-seq analysis were reliable. The transcript levels of surviving bacteria in tilapia primary macrophages were similar to those in mouse macrophages. Based on the findings, it was hypothesized that the noxious environment within the macrophage enhanced the signaling mechanisms, the energy transport capacity, the metabolic capacity of secondary metabolites produced by the macrophage, and the expression levels of virulence-related genes of S. agalactiae.