Ionizing radiation is used for various purposes, such as cancer treatment and medical diagnosis. As skin keratinocytes are frequently exposed to various radiation doses, the risk of developing skin diseases is also increasing. However, knowledge of the biological response of human keratinocytes to radiation doses and time-points is still limited despite its importance. Here, we characterized the proteomic and metabolomic changes in HEKn cells on day 0 and 2 after irradiation with control, 0.1, 0.5, and 2Gy to identify biological effects depending on IR dose and time. First, we found that the expression levels of proteins and metabolites involved in energy metabolism, DNA repair system, and epidermal cornification were changed following irradiation. In particular, fumarate and fumarate hydratase, which promote DNA repair, were significantly increased in response to irradiation with 2Gy on day 2. Furthermore, all doses of IR-induced proteomic changes correlated with epidermal cornification and inhibition of cell death on day 2 after irradiation. Using a human skin 3D full-thickness model, we observed dose-dependent increases in the cornified layer and the expression of involucrin. The multiomics signatures of cellular responses depending on IR dose and time may constitute a high-value resource, providing biological effects on IR applications.