As a high-impact educational practice, cooperative learning uses a structured group study to promote students' active learning. Currently, it lacks economical yet effective tools to facilitate the interactive nature of structured cooperative learning in regular classrooms. Here, we have established a mobile technology-based cooperative learning (MBCL) platform that comprises the 2018 iPad, Apple Pencil, LiveBoard, Google Forms, and Google Drive. We tested the MBCL platform in multiple undergraduate biology courses. During semester-long MBCL studies, the students engaged in cooperative learning to discuss a real-life issue or chapter-based contents. With the MBCL platform, the students' group study processes were shown on shared, visible electronic whiteboards that were updated in real-time, generating visible thinking and instant, interactive communication. The instructor was able to guide the students promptly to conduct knowledge integration and knowledge synthesis using tables and diagrams. The deep learning outcome was evident in the examples and quantitative analyses of students' whiteboard study results and team presentations. Thus, integrating innovative mobile technologies into high-impact teaching practices, exemplified by the MBCL platform, promotes deep learning in higher education.