Child neglect (CN) has been associated with eating disorders, but little is known about its prospective association with the eating habits (EHs) of children. This study aimed to assess the cross-sectional and prospective associations of baseline CN with six common EHs in Chinese primary schoolchildren. We analyzed two-wave data of 1102 children (aged 9.1 ± 0.5 years) in Wuhan, China. Baseline CN was investigated by the Child Neglect Scale. Baseline and follow-up EHs, including fruit, vegetables, milk, sugar-sweetened beverages, and high-calorie snack and breakfast consumption frequency, were assessed by the Food Frequency Questionnaires. The association of baseline CN with baseline/follow-up EHs was analyzed by the generalized linear model (GLM). The association of baseline CN with the change of EHs from baseline to follow-up was examined by the Generalized estimating equation (GEE) model. After adjusting for demographic characteristics, pubertal stage, and body mass index, GLM indicated that higher baseline CN was associated with lower frequency of consuming fruit/vegetables/milk/breakfast and higher frequency of consuming sugar-sweetened beverages and high-calorie snacks at baseline, while it was only associated with lower frequency of vegetables/breakfast consumption and higher frequency of sugar-sweetened beverages consumption at follow-up. GEE results indicated that children with higher CN had a more rapid increase for the frequency of fruit/milk/breakfast consumption and a steeper decrease for the frequency of sugar-sweetened beverages consumption. In conclusion, higher CN was associated with unhealthy EHs. Yet simultaneously, children with higher CN have more scope to promote the health of their EHs. Targeting and reducing CN may be a promising approach for future interventions to improve subsequent EHs.