A new isocoumarin, along with 10 known compounds, was isolated from the aerial parts of Aconitum gymnandrum. Their structures were elucidated by spectroscopic methods including extensive 1D and 2D NMR techniques. Among the known compounds, compound 11 was obtained as a natural product for the first time, which was previously reported as a synthetic product. In addition, compounds 1–5, 7 and 9 were tested for their cytotoxicity against four human cancer cell lines. The results showed that compounds 3, 4 and 7 displayed cytotoxicity against lung cancer A549 and gastric cancer MGC80, respectively, whereas 5 and 9 showed selective cytotoxicity against hepatocellular carcinoma HepG2.