The molecular mechanism of apoptosis induced by photodynamic therapy on human cervix cancer cells (HeLa) was studied. The method was to analyze the changes in FTIR spectrum of nucleic acids,proteins and lipids after photodynamic therapy. Compared with contrast group,the result shows that the peak intensity of the three spectrum lines (972,1083 and 1241 cm-1) representing nucleic acids decreases and the peak position shifts;the peak wave number of the spectrum lines (2923 cm-1 and 2957 cm-1) representing lipids increases and the peak intensity decreases noticeably;on the secondary structure of protein,the content of random coil and β turn increases dramatically and the content of α helix and β sheet decreases. It is concluded that photodynamic therapy leads to the damages of nucleic acids,proteins and lipids,as a result,inducing cancer cells apoptosis.