Driven by advances in high-throughput sequencing, artificial intelligence, and big data modeling, genomics is undergoing a profound paradigm shift from being experiment-driven to data-driven. This transformation not only reshapes the logic of knowledge production but also poses severe challenges to traditional ethical and governance frameworks. From the perspective of the philosophy of technology and centered on this “paradigm shift,” this paper first systematically outlines its technological trajectories and core features. It then delves into how this shift intensifies value tensions concerning privacy, equity, and human dignity, revealing their underlying philosophical foundations. The paper argues that the data-driven paradigm necessitates a profound reorientation in ethical governance from “risk mitigation” to “structural justice.” To this end, after a comparative analysis of the governance landscapes in the U.S., UK, and China, it proposes a five-pronged governance pathway, including dynamic consent, benefit sharing, and algorithmic audits. The study concludes that only by systematically embedding the principle of “structural justice” into institutional design can the development of genomics in the data-driven era be genuinely oriented toward public well-being and social equity.