Dietary patterns, such as selecting what food to regularly eat, may play role in reducing the incidence of metabolic syndrome (MetS). This study examined the causal relationships of Japanese dietary patterns and the relationship with the risk of MetS onset using a prospective cohort design. Data of annual health checks between 2008 and 2017 were analyzed, and middle-aged men and women (n=3,298 and 3,925, respectively) were followed up for 15,498 and 19,459 person-years, respectively. We investigated six dietary patterns using a questionnaire, and the participants were divided into low, middle, and high dietary score groups. During the follow-up period, cases of new-onset MetS were found in 698 men (21.2%) and 350 women (8.2%). Covariate-adjusted Cox proportional hazard models revealed that the risk of new-onset MetS was significantly lower in the male participants who responded that they “often eat vegetables” (HR: 0.77, 95% CI: 0.66–0.91). For dietary score, the male participants had significantly lower adjusted HRs of MetS onset in the middle-score group (HR: 0.80, 95% CI: 0.69–0.94) and high-score group (HR: 0.54, 95% CI: 0.41–0.72) compared to the low-score group. On the other hand, there was no association of each dietary pattern and dietary score with new-onset MetS among the female participants. This study found that favorable dietary patterns are associated with a lower risk of MetS; thus, education that aims to encourage a favorable diet may have an important role in reducing the incidence of MetS in middle-aged men.