Phytochemical investigation of the flowers of Inula japonica led to isolation of nine sesquiterpenoids, inujaponins A-I, as well as eighteen known ones. These sesquiterpenoids belong to six skeletal-types, including eudesmane, 1,10-seco-eudesmane, germacrane, guaiane, 4,5-seco-guaiane, and pseudoguaiane sesquiterpenoids. Their structures were established by extensive spectroscopic analysis. The absolute configurations of inujaponin A, eupatolide, and deacetylovatifolin were determined by Cu-Kα X-ray crystallographic analysis. Most of the isolated compounds exhibited potent cytotoxicity against HL-60, SMMC-7721, A-549, MCF-7, and SW-480 cancer cell lines, with IC50 values ranging from 1.57 to 22.58 μM. Some selected compounds also possessed significant inhibitory activity against LPS-induced NO production in RAW264.7 macrophages with IC50 values ranging from 1.42 to 8.99 μM.