This study was conducted to further explore the possible mechanism behind the finding that rural teachers are disadvantaged for participation in inquiry-based working compared to their urban counterparts. School organisation factors are the most obvious mediating variables since they can be easily connected with wider school regional features and with the behaviour of teachers. The contributions of two organisational factors, school research culture and school research infrastructure were studied. A multilevel structural equation model was developed based on data collected from 5566 Chinese teachers working in 114 primary schools. The results reveal the disparity in teacher-perceived school research culture and infrastructure between rural teachers and urban teachers. Perceived school research culture is positively related to teacher involvement in inquiry-based working, and mediates the rural-urban gap of teacher involvement in inquiry-based working at the between-level. The implications of these results and the theoretical, methodological, and practical contributions of this study are discussed.