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The aim of this study was to investigate the effects of project-based learning on the sixth graders' science process skills and problem-solving abilities under web-based PBL management system. In the study, quantitative methods were conducted and the experimental design with an experiment group and a control group was adopted. The subjects are 60 sixth graders from two classes in a school in Taipei city. This study conducted inquiry-based learning activities of the ecological ponds for subjects. One class, as the experiment group (n=30), was fostered through online project-based learning management system, while the other, as the control group (n=30), was taught via general nature science learning activities. The results were shown as follows: (1) Among the thirteen items of science process, the experimental group significantly outperformed than the control group in the subscales of Using Numbers (Quantifying), Interpreting Data, Communicating, Experimenting and the total score. (2) As to the problem solving abilities, the experimental group significantly outperformed than the control group in the subscales of Explain the Inference, Infer the Reason, Determine on the Solution, Prevent the Problems.