As mobile learning (ML) becomes more and more popular, teaching methods are gradually adapting to flipped classrooms or micro-flipped classrooms. Many studies have discussed the influence of ML-based flipped classrooms on students' learning in a macroscopic way. However, at the micro-level, the impact of these classrooms on students' emotional learning and cognitive flexibility requires further research--particularly of students of different levels of learning achievement (low, middle, and high). This study, carried out via both qualitative and quantitative methods, shows that in learning emotions, flipped classrooms based on ML had some effect on students' "self-directed learning" and "self-efficacy." Flipped classrooms did more to improve low achievers' intrinsic goals (learning motivation), metacognition (learning strategy), and resource management (learning strategy) than it did that of middle and high achievers. As for cognitive flexibility, results further indicated that flipped classrooms allowed low achievers the freedom to be more self-directed, helping them to feel a higher degree of "cognitive control" or "cognitive flexibility," thus improving their academic achievement. The results of this study lay a theoretical foundation for designing an effective flipped classroom environment with differentiated instruction in the future.