Chinese children are facing health challenges brought by chronic non-communicable diseases, such as physical problems and psychological related health problems. Childhood represents a critical life period when the long-term dietary and lifestyle behaviors are formed. It is necessary to survey the prevalence of suboptimal health status (SHS) among Chinese children and to research the relationship between SHS and lifestyles. This study aimed to examine the prevalence of SHS among Chinese children using a large-scale population survey sample covering school students and nonstudent children, and clarified the relationships between SHS and lifestyle factors using multi-level models controlled for the cluster effect of location and the confounding effect of demographics. Multi-level generalized estimating equation models were used to examine the relationships between SHS and lifestyle factors. Prevalence ratios (PR) and 95% confidence intervals (CI) were used to assess the strength of these relationships. Of the 29,560 children, 14,393 reported one or more SHS symptoms, giving a SHS prevalence of 48.69%. The prevalence of SHS for boys (46.07%) was lower than that for girls (51.05%). After controlling for the cluster effect of living areas and confounding effect of demographic characteristics, lifestyle factors associated with SHS were: less sleep duration, current smokers (PR = 1.085, 95%CI: 1.027–1.147), current drinkers (PR = 1.072, 95%CI: 1.016–1.131), children’ parents suffering from chronic diseases (PR = 1.294, 95%CI: 1.179–1.421), poor sleep quality (PR = 1.470, 95%CI: 1.394–1.550), stress (PR = 1.545, 95%CI: 1.398–1.707), negative life events (PR = 1.237, 95%CI: 1.088–1.406), hypertension (PR = 1.046, 95%CI: 1.009–1.084), unhealthy diet choice (PR = 1.091, 95%CI: 1.051–1.133) and irregular meal time (PR = 1.210, 95%CI: 1.163–1.259). Children who could exercise regularly (PR = 0.897, 95%CI: 0.868–0.927) and those with regular medical checkup (PR = 0.891, 95%CI: 0.854–0.929) were associated with lower prevalence probability of SHS. SHS has become a serious public health challenge for Chinese children. Unhealthy lifestyles were closely associated with SHS. Implementation of preventative strategies are needed to reduce the potential SHS burden associated with these widespread high-risk unhealthy lifestyle behaviors.