This research investigates the application of deep learning to college physical education, proposing an innovative teaching methodology that significantly improves outcomes by fostering students’ practical skills and innovation. We introduce a structured deep learning model encompassing four stages and twelve instructional steps, employing an “independent-cooperative-inquiry” modality in real-world teaching scenarios. Through empirical assessment in various T colleges, notable enhancements were observed in student attitudes toward physical education, collaborative spirit, and physical health, culminating in a 92% satisfaction rate with the teaching approach and an 85% boost in learning effectiveness. Adopting a deep learning-based pedagogy in physical education elevates teaching quality and enriches students’ comprehensive abilities, charting a new course for the pedagogical advancement in this field.