Recent studies have been indicated that genistein has a great inhibitory effect on liver, ovarian cancer and so on. A series of genistein derivatives was synthesized, which possessed the activity against lung A549 cell line and chondrosarcoma JJ012 cell line with an IC50 value of 26 μM and 7.53 μM, respectively. Follow genistein as lead compound, a series of azaisoflavone was synthesized by bioisosterism and subjected to structure- activity relationship (SAR) study of anticancer activity. The primary results was shown that azaisoflavones demonstrated good activity against lung A549 cell line and chondrosarcoma SW1353 cell line with an IC50 value of 8.9 μM and 5.8 μM, respectively. In this study, we described the SAR study of isoflavone and azaisoflavone and illustrated the activity of genistein derivatives against chondrosarcoma and lung cancer.