Studies have proven that merging hands-on and online learning can result in an enhanced experience in learning science. In contrast to traditional online learning, multiple in-classroom activities may be involved in an augmented-reality (AR)-embedded e-learning process and thus could reduce the effects of individual differences. Using a three-stage AR-embedded instructional process, we conducted an experiment to investigate the influences of individual differences on learning earth science phenomena of ''day, night, and seasons'' for junior highs. The mixed-methods sequential explanatory design was employed. In the quantitative phase, factors of learning styles and ICT competences were examined alongside with the overall learning achievement. Independent t tests and ANCOVAs were employed to achieve inferential statistics. The results showed that overall learning achievement was significant for the AR-embedded instruction. Nevertheless, neither of the two learner factors exhibited significant effect on learning achievement. In the qualitative phase, we analyzed student interview records, and a wide variation on student's preferred instructional stages were revealed. These findings could provide an alternative rationale for developing ICT-supported instruction, as our three-stage AR-embedded comprehensive e-learning scheme could enhance instruction adaptiveness to disperse the imparities of individual differences between learners.