The data presented in this article are related to the research article entitled “Isobarictags for relative and absolute quantitation (iTRAQ) -based proteomics for the investigation of the effect of HuganQingzhi on non-alcoholic fatty liver disease in rats” (Yao et al., 2017) [1] . This article describes the effect of HuganQingzhi on non-alcoholic fatty liver disease in rats at the level of the proteome (HFD: control, HH: control, HH: HFD, respectively). The field dataset is available to criticize or extended analyzes in public.