Hyperthermia treatment (44℃incubation) demonstrates advantages of low recurrence rate and high efficacy in treating viral warts. This study aimed to investigate the exact modulatory mechanism of hyperthermia treatment on immune response. We performed 4D-FastDIA quantitative proteomics to analyze differential protein expression and secretory profiles in HPV-positive epithelial cells following 37°C or 44°C incubation, to compare the changes before and after hyperthermia treatment. Two HPV-positive cell lines were included in this dataset, the group A1 and A2 were CaSki cells treated by 37℃- or 44℃-incubation separately; the group A3 and A4 were SiHa cells treated by 37℃- or 44℃-incubation separately.