Few studies have focused on clustering of unhealthy lifestyle behaviours among primary school children and potential associations with perceived and actual weight status. An index was constructed from adding up 13 unhealthy behaviours measured by survey responses. Multilevel linear regressions were used to analyse associations between child personal characteristics, perceived and actual weight status with the unhealthy lifestyle index among 11,157 children in primary schools across China. Parental and area factors were also taken into account, including education, weight status, physical activity, urban/rural and area socioeconomic circumstances. The unhealthy lifestyle index normally distributed, with 84.5% of children reporting between 2 and 6 unhealthy behaviours. Boys reported more unhealthy behaviours compared with girls (coefficient 0.32, 95%CI 0.26 to 0.37) and children in urban areas had fewer unhealthy behaviours than their rural counterparts (−0.29, 95%CI −0.56 to −0.03). An interaction revealed stronger ‘protective’ effects of living in cities for girls than boys, which were not explained by differences in child overweight/obesity. More unhealthy behaviours were characteristic of children in more affluent areas, and of those born to mothers and/or fathers with lower educational attainment. Children who perceived themselves as overweight or underweight both scored higher on the unhealthy lifestyle index. Unhealthy behaviours that could increase the risk of childhood obesity are common among Chinese primary school children, particularly among boys in cities, those in more affluent areas and with parents with lower education. There was no effect of actual weight status on number of unhealthy behaviours. Perceived, but not actual weight status, was also a significant correlate of unhealthy behaviours. Clustering of unhealthy lifestyle behaviours that could increase the risk of childhood obesity are common among Chinese primary school children, particularly among boys in cities, those in more affluent areas and with parents with lower education. Perceived, but not actual weight status, was also a significant correlate of unhealthy lifestyle. This has important implications for public health because understanding clustering of unhealthy lifestyle behaviours can be used to assist in the development of targeted obesity prevention initiatives.