The purpose of this study was to find out the effectiveness of metacognitive instruction model on the changes of science concepts, when it was applied to 6th grade students. To do this, students were tested with the achievement of molecules and molecular motion concepts and metacognitive self-regulation test as a pretest. Based upon metacognitive instruction model and student`s conception, instruction program were developed. This metacognitive strategy Program was applied to the experimental group and expository teaching was applied to the comparison group (followed the order and method in authorized science textbook and teacher`s handbook). When planned lessons were finished, students were given a post-test to find conceptual change. After six months students were given a test again to find retention effect. There was a significant difference in conceptual change and retention between comparison group and experimental group by treatment at p$lt;.05 level. The difference between comparison group and experimental group was especially significant, when the situation of test item wasn`t similar to that of the textbook. Metacognitive instruction model was more effective to high group than low group in metacognitive self-regulation level on conceptual chance and retention. So the metacognitive strategy Played an important role in conceptual change and retention. And we can recognize that the students who take part in the metacognitive lessen can apply the corrected concept to the other concrete situation because they can understand new concept accurately by metacognitive strategies. And we can guess that high group in metacognitive self-regulation level can team metacognitive strategy easily but relatively low 7:roue students have some trouble in learning new strategy.