A new algorithm is proposed for accelerating chemical structure similarity search by means of graphic processing unit technology. Experiments demonstrate that the new algorithm is on average more than 120-times faster than the one implemented in conventional central processing unit technology. In order to test the generality of the new algorithm, it has been applied in seven progressive virtual screening experiments on NCI/DTP 60 human cancer cell lines data. The progressive virtual screening results show that the technology can select 10-20% compounds for screening to get 70-80% intrinsic hits for a given chemical library and target.