The integrated model of rumination argues that two trait factors—negative thinking habits and processing modes—get people stuck in maladaptive rumination. There is little evidence showing whether these factors influence the daily dynamic associations between rumination and negative moods. To address this, in this study, we conducted an experience-sampling method on Japanese university students. We recruited 92 Japanese university students and assessed their daily rumination and negative affect (NA) eight times a day for seven days. We examined the effects of habits and processing modes on the dynamic associations between rumination and negative moods using dynamic structural equation modeling. We found that individuals were more likely to ruminate when they experienced NA. However, contrary to previous findings, this study’s participants did not experience NA after engaging in rumination. Moreover, we did not detect any significant trait factor effect on these dynamic associations. Our findings imply that individuals are more likely to engage in rumination after experiencing NA, but the reverse association, particularly the autoregression of rumination, may not be maintained in natural daily life. Furthermore, negative thinking habits and processing modes may not influence the daily dynamic associations between rumination and NA among Japanese university students.