Background: Seasonal influenza epidemic occurs every year in Guangzhou, which can affect all age groups. Young children are the most susceptible targets. Parents can decide whether to vaccinate their children or not based on their own consideration in China. The aim of this study was to identify factors that are important for parental decisions on vaccinating their children against seasonal influenza based on a modified health belief model (HBM). Methods: A cross-sectional study was conducted in Guangzhou, China. A total of 335 parents who had at least on child aged between 6 months and 3 years were recruited from women and children′s hospital in Guangzhou, China. Each eligible subject was invited for a face-to-face interview based on a standardized questionnaire. Results: Uptake of seasonal influenza within the preceding 12 months among the target children who aged between 6 months and 36 months was 47.7%. Around 62.4% parents indicated as being "likely/very likely" to take their children for seasonal influenza vaccination in the next 12 months. The hierarchical logistic regression model showed that children′s age (odds ratio [OR] =2.59, 95% confidence interval [CI]: 1.44-4.68), social norm (OR = 2.08, 95% CI: 1.06-4.06) and perceived control (OR = 2.96, 95% CI: 1.60-5.50) were significantly and positively associated with children′s vaccination uptake within the preceding 12 months; children with a history of taking seasonal influenza vaccine (OR = 2.50, 95% CI: 1.31-4.76), perceived children′s health status (OR = 3.36, 95% CI: 1.68-6.74), worry/anxious about their children influenza infection (OR = 2.31, 95% CI: 1.19-4.48) and perceived control (OR = 3.21, 95% CI: 1.65-6.22) were positively association with parental intention to vaccinate their children in the future 12 months. However, anticipated more regret about taking children for the vaccination was associated with less likely to vaccinate children within the preceding 12 months (OR = 0.21, 95% CI: 0.08-0.52). Conclusions: The modified HBM provided a good theoretical basic for understanding factors associated with parents′ decisions on their children′s vaccination against seasonal influenza.