Against the converging policy priorities of coordinating education, science and technology, and talent development; improving the quality of basic education; and accelerating educational digitalization, conventional high-school governance based on administrative directives and rigid quantitative assessment is increasingly ill-suited to diversified university selection, the long-term development of exceptional talent, and the integration of values into science and engineering education. This study examines the governance reform undertaken by Shenzhen Gezhi High School, which has adopted aerospace science and innovation as a distinctive educational focus. The reform pursued two interrelated aims: improving science education and establishing whole-school, whole-process education, understood as an institution-wide approach spanning organization, teachers, curriculum, evaluation and multi-stakeholder collaboration. Guided by the school’s medium- and long-term development plan, governance shifted from unilateral administrative control to empowerment-oriented governance, characterized by devolved authority, coordinated resource allocation and collaborative participation. The study draws on action research, continuous observation across two campuses, stratified semi-structured interviews, and quantitative evidence-based analysis conducted over three consecutive years. It identifies five interrelated constraints within the previous model: fragmented organizational coordination, inflexible teacher evaluation, imbalanced differentiated curriculum provision, score-dominated student assessment, and restricted external collaboration. In response, the school developed an integrated framework comprising organization, teacher development, curriculum, digital evaluation, and multidimensional collaboration. The values associated with crewed spaceflight and “Two Bombs, One Satellite”—especially patriotism, dedication, scientific self-reliance, and collective endeavor—were incorporated into aerospace-related learning activities. Longitudinal evidence indicates improved cross-campus resource use, stronger interdisciplinary teaching capacity, more coherent pathways for exceptional talent, and greater institutional distinctiveness. The case provides a locally grounded model for public school groups seeking to combine science education, digital governance, values education and secondary-university articulation.