The purpose of this research was to survey middle school students' preference for science and its causal factors, so as to analyze the causal relationships between them. Preference for science and its causal factors were defined theoretically, and a theoretical model was constructed to measure them and analyze the causal relationship by structural equation modeling. According to the theoretical model and a pilot test, a questionnaire was developed with three parts; the background information of a respondent, the preference for science, and the causal factors of preference. The questionnaire was administered to one class per grade of randomly selected 8 middle schools from 4 areas across the country, and 819 students' data were collected. Preference for science was defined as a state of mind. It revealed to what extent, and how, one likes science. It consisted of 3 categories - 'emotional response', 'behavioral volition', 'valuational comprehension', and each category was divided into two subcategories. Causal factors affecting the preference for science consisted of three categories - personal, educational and social factors, and each was divided into 2 or 3 subcategories. Middle school students' preference for science was middling as a total. Curiosity about contents of science and valuation of science were high, comparatively, but behavioral volition about science was especially low. Students' responses to the causal factors were relatively high in every educational factor and sociocultural valuation of social factors, but relatively low in socioeconomic rewards of social factors, and especially low in personal factors. The causal relationship about the preference for science was investigated by multiple regression analysis and path analysis, using the structural equation model. Multiple regression analysis about the preference for science and its causal factors revealed important factors. The important factors were personal ability, the personal traits, rewards in school science, and contents of school science in order of magnitude of standardized regression coefficient ${\beta}$. Stepwise regression analysis with each of the subcategories of the preference for science as dependent variables showed what factors were important in each subcategory. According to the result of structural equation modeling, personal factors affected 'emotional response' and 'behavioral volition' directly, and social factors affected 'valuational comprehension' directly. Educational factors affected all categories of the preference for science by influencing not only 'emotional response' and 'valuational comprehension' directly, but also 'behavioral volition' indirectly. The way to promote middle school students' preference for science was suggested, based on the analysis result.