Internal/external frame of reference (I/E) is widely used, but there is no examination across gender. Thus, this study aims at comparing the internal/external frame of reference (I/E) model of different gender in math field and science field and uses the LISREL software to analyze the data of Taiwan eighth grade students in TIMSS 2003, which means 5379 students were selected as samples. Results show that: 1. The data of different gender Taiwan eighth grade students in TIMSS 2003 supports I/E model. 2. The boys are significantly higher math self-concept and science self-concept than the girls. However, there is no difference in math achievement and science achievement between two genders. 3. I/E model only explains part of the differences of academic self-concept between two genders. There are others factors needed to discover for future study.