The HPLC fingerprint of Phyllanthus urinaria from different habitats, different harvest times, different parts was determined and compared by RPHPLC. The comparative study was done with the HPLC fingerprint of Yexiazhu Capsules also. The representative HPLC fingerprint of P. urinaria was established. The results showed: (1) There were 18 mutual peaks, four of which were identified by reference substance. The similarity of 11 samples from different habitats was in the range of 0.89 to 0.99. (2) The similarity of 7 samples from different harvest times was greater than 0.94. The peak area of most mutual peaks increased with growth period, the highest was in 5 October. It was suggested the best harvest time was on early October annually. (3) The similarity of samples from different parts was analyzed and evaluated. The similarity of leaf and fruit was higher in the range of 0.98 to 0.99, and the similarity of root and stem was in the range of 0.86 to 0.87. Lower content of components in root and stem brought about the difference in similarity. It was suggested only collecting the aerial parts. (4) The chemical constituents of Yexiazhu Capsules were nearly consistent with that of reference herb of P. urinaria, but the peak area of some peaks varied very much because of processing of Yexiazhu Capsules. So, this method is simple, accurate, and reproducible, which can be used for the quality control and evaluation of P. urinaria and its Chinese proprietary medicines.