This study investigated developmental changes in metacognitive strategies during elementary school years and examined the effects of intrinsic motivation on metacognitive strategies. A total of 113 Japanese elementary school children participated in a three-year longitudinal survey with eight times measurement occasions. Multilevel modeling analyses showed that metacognitive strategies would linearly increase over three years. Intrinsic motivation was also related to metacognitive strategies in two ways: the initial status of intrinsic motivation was associated with the average level of metacognitive strategies. Further, the deviations from the baseline of intrinsic motivation were related to changes in metacognitive strategies. This suggests that intrinsic motivation impacts the development of metacognitive strategies.