Two key biosynthetic intermediates (pumiloside and strictosamide) of camptothecin were isolated. A high performance liquid chromatography-ultraviolet (HPLC-UV) method was developed to determine four main alkaloid compounds (pumiloside, strictosamide, camptothecin and 10-hydroxycamptothecin) and estimate two minor compounds (deoxypumiloside, 9-methoxycamptothecin) simultaneously in different parts of Camptotheca acuminata, with a good linearity and R2 > 0.999 for all curves. The results indicated that there was a positive correlation between the two key intermediates (strictosamide and pumiloside) and camptothecin in vivo. The speculation that the root was the synthetic position of camptothecin in vivo was confirmed. The rate-limiting step of camptothecin biosynthesis was estimated the step from pumiloside to deoxypumiloside based on its concentration fall sharply.