Climate change has significant economic impact on livestock production including poultry. Heat stress can adversely affect the health and performance of poultry. Genetic improvement by selective breeding on more climate-resilient poultry could contribute to the mitigation of negative impact on food security by heat stress. Here we utilized an experimental animal model of two highly inbred chicken lines with distinct responses to heat stress and virus infection (more-resilient Fayoumi and more susceptible Leghorn lines), and a commercial layer line (Hy-Line Brown) to elucidate genetic control of host response to Newcastle disease virus (NDV) infection under heat stress. The heat stress and immune-related tissues including liver, muscle, hypothalamus, spleen in Fayoumi and Leghorn lines were collected at multiple time points during the course of treatment (heat stress and NDV). An “omic” approach including transcriptome, proteome, metabolome, and epigenome on these tissues were conducted. Bioinformatic analysis on these “omic” data identified potential candidate genes, signaling pathways, and gene network that are associated with host response to heat stress under NDV infection. In addition, a genome-wide association analysis was conducted in Hy-Line Brown to identify genomic regions affecting physiological parameters that are indicators of host response to heat stress. This integrative and comprehensive analysis have generated many valuable novel information that can be used in further understanding molecular and cellular mechanisms of host response to heat stress, and aiding potential selective breeding for more resilient animals.