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This study aimed to examine whether the relationships among family resources, school climate, learning participation, science attitude, and science achievement are different between primary school students and junior high school students within one educational system. The subjects included 4,181 Grade 4 students and 5,074 Grade 8 students who participated in TIMSS 2003 in Taiwan. Using structural equation modeling, the results showed that family resources had significant positive effects for both groups of learners. Furthermore, a context effect for the structural relationship between school climate, learning participation, and science achievement was revealed. In the primary school context, Grade 4 students who perceived positive school climate participated in school activities more actively, and had better science performance. However, in the secondary school context, learning participation had a negative impact and led to lower science achievement. The implications about this result in relation to the characteristics of the two educational contexts in Taiwan were further discussed.

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