This study investigated the effects of metaconceptually-enhanced, simulation-based inquiry learning on eighth grade students' conceptual change in science and their development of science epistemic beliefs. Two experimental groups studied the topics of motion and force using the same computer simulations but with different simulation guides: one enhanced with metaconceptual scaffolding, while the other was not. The findings led to the following conclusions: (a) metaconceptual scaffolding enhanced simulation-based learning by significantly reducing science misconceptions, but it was not as effective in changing students' mental models which consisted of multiple interrelated key concepts; (b) students' beliefs about the speed of learning and the construction of knowledge were strong predictors of conceptual change learning outcomes; (c) epistemologically more mature students did not benefit more from metaconceptual interventions than those with less mature beliefs; (d) further interventions are needed to promote the development of students' science epistemic beliefs in inquiry learning.