Two new guaiane-type sesquiterpene glycosides, atractylodes guaianoside I (1) and atractylodes guaianoside II (2), along with eleven known sesquiterpenes (3-13), were isolated from Atractylodes Japonica Koidz. ex Kitam. The structures of these two new compounds were elucidated by extensive spectroscopic analyses and mass spectrometric techniques. And their absolute configurations were confirmed by electronic circular dichroism (ECD) calculations. In addition, the isolated compounds were evaluated for their cytotoxic activities against three cancer cell lines HT-29, A-549, and MCF-7. Results showed that new compound 2 had inhibitory effects on three types of cancer cells, while new compound 1 only had inhibitory effects on HT-29 and MCF-7.