The association of free sugars intake with metabolic syndrome (MetS) is controversial. This study aimed to examine the association between free sugars intake and risk of MetS in Chinese adults. The data were from seven waves of the China Health and Nutrition Survey (2000–2018), a longitudinal and open prospective cohort study. Dietary intake was calculated based on the data collected by consecutive 3-day 24-h dietary recalls combined with household weighing for foods or condiments. Cox proportion hazard regressions and restricted cubic spline (RCS) were performed to explore the associations between free sugars intake and the risk of MetS. The present study selected 12,048 adults aged 18 years and above. During a median (IQR) follow-up of 9.0 (7.0, 15.0) years with 131,844.0 person-years, 3970 (32.95%) MetS occurred. After adjusting for all potential confounders, compared to adults with free sugars intake of <5 g/day group, adults with free sugars intake of 5–20 g/day were associated with a higher risk of MetS (HR, 1.094; 95% CI, 1.009–1.186). No significant association was observed between free sugars intake of >20 g/day and the risk of MetS (HR, 1.011; 95% CI, 0.800–1.277). There is an urgent need to pay attention to the intake of free sugars and comprehensive measures such as the improvements in the processing of sugary foods, and sugar composition should be included on food nutrition labels to control intake of free sugars in China.