Type I interferons (IFNs) play essential roles in establishing and modulating host defense against microbial infection via induction of IFN-stimulated genes (ISGs) through Janus kinase (JAK)–signal transducer and activator of transcription (STAT) signaling pathway. However, dysregulation of IFNs production and function could also mediate immune pathogenesis such as inflammatory autoimmune diseases and infectious diseases via aberrantly activating inflammatory responses or improperly suppressing microbial controls. Thus, IFN responses need to be tightly regulated to achieve protective immunity against microbial infection while avoiding harmful toxicity caused by improper or prolonged IFN signaling. Multiple levels of cellular and molecular events act in a cooperated manner to regulate IFN responses, in especial, post-translational modification (PTMs) of signaling molecules and epigenetic modification of gene expression programs are two important mechanisms for regulation of IFN signaling and thus critical for orchestrating IFN-mediated host immune response to the complex pathogenic or environmental stimuli. Conventional PTMs such as phosphorylation and polyubiquitylation, as well as numerous other PTMs including acetylation, ISGylation, SUMOylation and methylation have been shown to potently modulate type I IFN signaling transduction via targeting distinct signaling steps or components. Moreover, epigenetic mechanisms, such as histone modification, DNA methylation, non-coding RNAs play critical roles in regulating chromatin structure and function, leading to flexible and dynamic gene expression patterns downstream type I IFN signaling. Herein, we summarize the recent advances in the PTMs and epigenetic mechanisms in regulation of type I IFN signaling and responses. The involvement of dysregulated IFN signaling in inflammatory and autoimmune diseases are also discussed.