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Controlling heat stress (HS) is a global challenge for the dairy industry. In this work, an integrated metabolomics and lipidomics approach using 1H nuclear magnetic resonance (NMR) and ultra-fast LC–MS in combination with multivariate analyses was employed to investigate the discrimination of plasma metabolic profiles between HS-free and HS lactating dairy cows. Here we provide the information about the acquiring and processing of raw data obtained by 1H NMR and LC–MS techniques. The data of present study are related to the research article “Identification of diagnostic biomarkers and metabolic pathway shifts of heat-stressed lactating dairy cows” in the Journal of Proteomics (Tian et al., J. Proteomics, (2015), doi:10.1016/j.jprot.2015.04.014).