In this study, we examined the longitudinal reciprocal relationships among mastery goals, autonomous motivation, and motivation instability. In the hierarchical model of motivation, mastery goal for overall course subject learning has been positioned at the contextual level, while autonomous motivation and motivation instability during a specific class session were positioned at the situational level. A longitudinal online survey of university students in five asynchronous online classes at a Japanese university was conducted at three time points in one semester. A total of 218 university students participated in the study. A cross-lagged panel model was constructed and analyzed by structural equation modeling. The results showed that the mastery goal at Time 1 was positively associated with autonomous motivation at Time 2. In addition, the mastery goal at Time 2 was positively associated with autonomous motivation at Time 3 and negatively associated with motivation instability at Time 3. These results indicate a top-down effect of mastery goal at the contextual level on situational motivation, which is located lower in the hierarchical model. Furthermore, autonomous motivation at Time 2 was positively associated with the mastery goal at Time 3. This indicates a bottom-up effect, in which contextual motivation, which is located higher in the hierarchical model, can be altered by situational motivation in the classroom. The results of the study clearly show a longitudinal reciprocal relationship between contextual level motivation and situational level motivation.