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This study examined the complex relationship of the dynamics of student’s positive affect (PA) and negative affect (NA) with their learning goal achievement (LGA) using the dynamic structural equation modeling (DSEM). Based on the 32 days of intensive longitudinal data of student’s affect and LGA from the HBAPA data, we found that students had equilibrium of affect and LGA over time with no systematic changes, while the observations were significantly fluctuated. There was a significant relationship between the affect and LGA with no cross-lagged relationship between PA and NA. Three covariates (i.e., age, number of semesters studied, depression) were significantly related with the dynamics of affect and LGA.