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Based on the self-determination theory(SDT), the current study discussed whether the integration of autonomy-supportive and structure-supportive teaching strategies could be effective in improving students’ science learning in web-based learning environment. This experimental designed study with pre- and post measurements was conducted in Fall semester, 2017. 104 5th grade students from three classes and their science teachers from a medium primary school in China participated into this study. Results showed that the students in a learning condition with both autonomy and structure support outperformed than others who were in the condition with autonomy support only. The findings indicated that even in a web-learning environment, a well-structured class was very critical and fundamental, where the effects of autonomy support could be optimized.