Transcriptomic studies in fish have considerably contributed to understanding the host responses under viral hemorrhagic septicemia virus (VHSV) infection. However, changes from the perspective of the pathogen and host-pathogen interactions have been relatively underestimated. Given that VHSV genes can be poly-adenylated during replication, this study investigated the global changes from both VHSV and host perspectives using the host transcriptomic data. To achieve this, we utilized transcriptomic data from VHSV infected flounder obtained at different water temperatures (13 °C and 20 °C). We collected the sequence reads belonging to VHSV through an bioinformatic pipeline developed especially for this study. The VHSV reads were used to construct the consensus reference genome and to investigate the expression of VHSV genes and the frequency of variants under different water temperatures. In addition, both linear and logarithmic scales of VHSV transcription levels, along with host transcriptomes, were used to understand pathogen-host interaction through weighted correlation network analysis (WGCNA). The results revealed that VHSV transcription can exceed 5% of host transcriptome during the infection. Single nucleotide variants (SNVs) appeared more frequently in 13 °C groups than in 20 °C groups. While VHSV can replicate at both 13 °C and 20 °C, host transcriptomic responses were notably different, with stronger immune responses and more frequent VHSV genetic changes observed at a lower temperature. This suggests that VHSV infection at low water temperatures significantly influences both the host transcriptional changes and pathogen. Through WGCNA, numerous genes in the module that correlated with VHSV reads on a linear scale were found to be related to cytoskeleton modulation and viral activity. By contrast, the gene module (black) correlated with VHSV reads on a logarithmic scale was strongly associated with host immune responses, such as TNF signaling, necroptosis, and the NF-kappa B signaling pathway. The dual RNA-seq approaches developed in this study will immensely enhance our understanding of host-pathogen interactions across different temperatures.