This mixed-method study, employing inquiry-based science teaching theory, delves into the interaction of English Medium Instruction (EMI) and scientific inquiry by investigating science teachers' understanding and perceptions of conducting inquiry-based science activities in EMI classrooms. Drawing on a questionnaire of 166 EMI science teachers and in-depth individual interviews with five of them, the findings suggest that these EMI science teachers encountered similar challenges to other science teachers teaching science in their first languages through an inquiry-based approach. They were found to hold a ­scientific ­method-oriented understanding of inquiry-based science teaching and a conflict between Chinese learning culture and ­inquiry-based science learning culture. Furthermore, the findings indicate that EMI science teachers faced additional challenges in inquiry-based science classrooms in the EMI context, including (a) the tension between passive English learning and the mutual learning of scientific inquiry and English, and (b) the contradictory stance between ­inquiry-based science teaching and EMI policy. This study has implications for policymakers in terms of the teaching and provision of ­inquiry-based science in the EMI classroom.