Objective: This study explores the current situation of anxiety disorder of pre-schoolers and assesses the association between family structure and anxiety disorder (AD) among pre-schoolers in Chongqing, China.Methods: This is a cross-sectional study of 499 main fosterers of children aged 3–6 years who completed the 28-item Chinese version of the Spence Pre-school Anxiety Scale (PAS). Multinomial logistic regression with three models was used to assess the association of the family structure with the different AD.Results: The prevalence of AD was 31.46%, whose score of PAS were more than 48. Among the five different PAS sub-scales, the prevalence of obsessive-compulsive disorder (OCD) was the highest (50.10%), followed by separation anxiety disorder (SAD, 39.28%), fear of physical harm (FPH, 37.68%), generalized anxiety disorder (GAD, 33.47%), and social phobia (SP, 25.85%). Pre-schoolers from inter-generational families were more probably have AD than those from nuclear families (OR = 3.73, p < 0.05). The participants from inter-generational families were more likely to have SAD (OR = 3.39, p < 0.05), FPM (OR = 2.80, p < 0.05), or OCD (OR = 2.40, p < 0.05), in comparison with participants from other family structures.Conclusion: Anxiety disorder among pre-schoolers aged 3–6 in Chongqing is widespread. Pre-schoolers from inter-generational families were more probably have AD, SAD, FPM, and OR and pre-schoolers from stem families may be less likely to have SAD compared with those from nuclear families. Relieving the anxiety of pre-schoolers may be possible with additional interventional efforts in inter-generational families.