The rhizome of Atractylodes ovata De Candolle is rich in essential oils, which are usually removed by processing. In this study, anti-oxidative abilities of essential oils and aqueous extracts of A. ovata rhizome were explored, and the influence of processing on the anti-oxidative abilities was examined. Essential oils and aqueous extracts of A. ovata were extracted by boiling water and steam distillation, respectively. Quality of these two A. ovata samples was controlled by HPLC and GC-MS system, and anti-oxidative abilities were then evaluated. Results showed that surface color of A. ovata turned to brown and chemical components were changed by processing. Contents of both atractylon and atractylenolide II decreased in the essential oils, but only the contents of atractylon decreased by processing. Atractylenolide III increased in both A. ovata samples. However, A. ovata essential oils displayed stronger anti-oxidative abilities than aqueous extracts in DPPH-scavenging, TBH-induced lipid peroxidation and catalase activity assays. Moreover, the bioactivity of essential oils from raw A. ovata was stronger than oils from processed A. ovata. On the other hand, cytotoxicity of A. ovata essential oils was stronger than that of aqueous extracts, and was more sensitive on H9C2 cell than NIH-3T3 and WI-38 cells. In contrast, stir-frying processing method increased cytotoxicity of essential oils, but the cytotoxicity was ameliorated when processed with assistant substances. The results suggested that phytochemical components and bioactivity of A. ovata were changed after processing and the essential oils from raw A. ovata showed better anti-oxidative and fewer cytotoxicity effects.