While the past two decades have witnessed a surge of studies on the researcher identity of English as a Foreign Language (EFL) academics, research on how the intertwined connections between EFL academics and the larger ecological system within an institution affect their researcher identity construction remains relatively scarce. Utilizing a three-tier system framework, this study seeks to address this gap by exploring how EFL academics (micro level) in China navigate the complexities of aligning their researcher identity (re)construction with institutional practices (meso level) of a national policy (macro level). Adopting a case study design, this study collected and triangulated data from three sources: semi-structured interviews, narrative frames, and document analysis. Data analysis revealed that there were (mis)alignments between EFL academics' research expectations of national research policy and interpretations of research policy at the institutional level, and participants adopted different responses in re-adjusting their research practices to align with research policy. The study implies the need for university administrators to take into account academics' disciplinary features, research values, and needs when implementing institutional research policies. Such an orientation provides more opportunities and resources to shape, rather than break, the researcher identities of EFL academics and ultimately facilitate the sustainable development of higher education.