Background: The clearance or transcriptional silencing of integrated HBV DNA is crucial for achieving a functional cure in patients with chronic hepatitis B (CHB) and reducing the risk of hepatocellular carcinoma (HCC) development. The PLC/PRF/5 cell line is commonly used as an in vitro model for studying HBV integration. In this study, we employed a range of multi-omics techniques to gain a panoramic understanding of the characteristics of HBV integration in PLC/PRF/5 cells. Methods: Transcriptome long-read sequencing (ONT) was conducted to analyze characterize the transcriptional activity of different HBV DNA integrations in PLC/PRF/5 cells. Additionally, data pertaining to epigenetic regulation such as whole-genome bisulfite sequencing (WGBS), histone chromatin immunoprecipitation sequencing (ChIP-seq), and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were collected to investigate the potential mechanisms associated with the transcriptional regulation of integrated HBV DNA. Result: Our findings indicate that transcriptional activity of integrated HBV DNA in PLC/PRF/5 cells is influenced by methylation levels of the surrounding host genome near the integration site. The result indicated that elevated methylation of the adjacent host genome adversely impacts transcription activity of integrated HBV DNA. Furthermore, we observed a positive association between histone modification H3K4me3 and the transcription of integrated HBV DNA. These results suggest that host may regulate transcriptional activity of integrated HBV DNA through DNA methylation and histone modifications. Potentially leading to the silencing of integrated HBV DNA. Conclusion: Our study brought a better understanding on the transcriptional regulation of integrated HBV DNA. This knowledge can be valuable in the development of novel strategy for functional cure of CHB.