The past few decades have seen a boom in English-medium instruction (EMI) in Chinese universities. Despite growing research interest in EMI policy and practices in China, little is known about how students' motivation to study in the EMI programs is influenced by EMI policy and its implementation at the meso and micro levels. This study addresses this gap by examining an EMI program at a Chinese medical college. Through a survey of 118 students and interviews with 10 students and 6 teachers, we investigated students' EMI learning motivation, how and why it changed over time, and different stakeholders' perceptions of the EMI implementation. The questionnaire and interview data were triangulated with textual analysis results of institutional EMI policy documents. It was found that students' motivation generally declined over the course of EMI study and was often influenced by implementation factors such as pedagogical practices, assessment-related policies, and incentive strategies. Interactions and contradictions between the EMI policy goals, EMI implementation at different levels and students' motivation change were also analyzed through the Activity Theory lens to shed light on how higher education institutions could better sustain students' EMI motivation and enhance the quality of EMI programs.