The PISA study offers an excellent opportunity to see more clearly what extent to each region or country is doing and where there might be room for improvement. Generally speaking, the students of 15-year-old in Taiwan are doing well in PISA 2006. In terms of quality and equity in the performance of students and schools, it is important to interpret the performance variation among schools jointly with the performance variation between students. Therefore, the purpose of this study is to examine to what extent Taiwan achieves in moderating the relationship between socio-economic background and student performance. Also, exploring what else factors can explain effectively the variation of students performance except for socio-economic background. To understand the quality and equity in science literacy for Taiwan students’ performance, the study attempts to discover some explanatory variables which can mediate the impact of socio-economic status on students’ performance in science.