The rapid development of information technology has prompted the innovation of the education model, in which the flipped classroom, as a new type of teaching mode, reconfigures the structure of traditional classroom teaching and emphasizes the students’ leading position in the learning process. In this context, cultivating students’ independent learning skills is fundamental, but motivating students to learn independently has become a significant challenge for educators. This study explores the motivation mechanism of students’ independent learning based on the flipped classroom model in the context of informationization only to provide theoretical and practical support for improving students’ independent learning ability. The theoretical framework of independent learning incentives is defined through a literature review and empirical research methods, and a series of incentives are designed and implemented in this study. The study collected data from 300 students, and by comparing the assessment results of independent learning ability between the experimental group and the control group before and after the implementation of the incentive mechanism, it was found that the students in the experimental group had improved their independent learning ability, in which the average time of independent learning had increased by 15%. The effectiveness of learning had been improved by 20%. Effective incentive mechanisms can better enhance students’ independent learning ability, and it is recommended that educators adopt the incentive mechanism constructed in this study in flipped classroom teaching to promote the improvement of students’ independent learning ability.