This study was designed to explore pupils¡¦ argumentation ability and understanding about the nature of science during the argumentation activities. The method of quasi-experiment with non-equivalent group pretest-posttest design was employed. One class of 5th graders (N=22) was selected as the experimental group with 8-week argumentation instruction, and the other class (N=22) with the similar backgrounds taught with traditional instruction was served as the control group. The instruments of Argumentation Ability Test and Nature of Science (NOS) questionnaire were used in pre- and post-tests. The result indicated that the experimental group students outperform their counterparts in argumentation ability. However, there is no significant difference between the two groups on their understanding about the nature of science. Further analysis reveals that the experimental students with contemporary view of NOS make progress differently from those who are with traditional view of NOS.