By measuring students' attitudes towards science using Rasch modelling, the present study investigated the factors related to elementary students' attitudes toward science at both the individual- and school- levels using HLM in China, where students are often reported to have high achievement in science with below-average attitudes towards the subject. While little has been explored of the related field, it is a phenomenon worth noticing. By analysing a sample of over 6000 fifth graders from 66 schools, we found that most variance in student attitudes towards science occurred at the student level, but variations among schools were also significant. At the student level, gender, socioeconomic status, and teacher-student relationship were significantly associated to attitudes toward science. Male students, who have better socioeconomic status and perceive better teacher-student relationships, adopt more positive attitudes towards science. At the school level, the factors explored did not show significant correlation with students' attitudes towards science. The findings are discussed, and implications for future research and science teaching have been provided.