The integration of physical education and academic education serves as the core guiding principle for sports education development in the new era, providing clear direction for reforming public physical education courses in higher education institutions. As a vital component of quality education, these courses bear the important mission of enhancing students’ physical fitness, cultivating sports skills, and fostering sports literacy. However, the current public physical education curriculum system in universities faces challenges such as insufficient alignment with sports education objectives, monotonous content, weak practical components, and one-sided evaluation mechanisms, making it difficult to meet the requirements of the integration of physical education and academic education. From the perspective of this integration, this paper analyzes existing issues in the public physical education curriculum system and proposes optimization strategies across four dimensions: curriculum philosophy innovation, content restructuring, structural optimization, and evaluation improvement. The aim is to establish a public physical education curriculum system that aligns with the integration of physical education and academic education, thereby enhancing teaching quality and promoting students’ all-round development.