This study examined the prevalence of suboptimal health among Chinese adults based on a large-scale national survey and clarified the relationship between suboptimal health and lifestyle factors. We used multi-level generalized estimating equation models to examine the relationships between suboptimal health and lifestyle factors. Of the 48,978 respondents, 34,021 reported one or more suboptimal health symptoms, giving a suboptimal health status prevalence of 69.46%. After controlling for the cluster effect of living areas and confounding effect of demographic characteristics, factors associated with suboptimal health were: current smoking (odds ratio (OR) = 1.083, 95% confidence interval (CI): 1.055-1.111), drinking alcohol (OR = 1.075, 95% CI: 1.025-1.127), family history of disease (OR = 1.203, 95% CI: 1.055-1.111), sleeping <6 h per day (OR = 1.235, 95% CI: 1.152-1.256), poor sleep quality (OR = 1.594, 95% CI: 1.515-1.676), stress (OR = 1.588, 95% CI: 1.496-1.686), negative life events (OR = 1.114, 95% CI: 1.045-1.187), unhealthy diet choices (OR = 1.093, 95% CI: 1.033-1.156), and not regularly having meals at fixed hours (OR = 1.231, 95% CI: 1.105-1.372). Respondents who exercised regularly had lower odds of having suboptimal health status (OR = 0.913, 95% CI: 0.849-0.983). Suboptimal health has become a serious public health challenge in China. The health status of the population could be effectively improved by improving lifestyle behaviors.