Objective To understand the timely vaccination rate of the first dose of hepatitis B vaccine (HepB1) and its related factors in some areas of western China. Methods A cross-sectional study with three-stage stratified random sampling method was conducted from September to October in 2011, and a total of 2 999 children aged 0~35 months in 14 counties of western China were chosen to provide information on their first dose of hepatitis B vaccine from "vaccination certificate". Results The vaccination rate of HepB1 and the timely vaccination rate of HepB1 were 99.3% and 68.5% respectively. Univariate analysis showed that gender, ethnicity, age, birth place, household net income per capita, caregiver′s educational level, and low birth weight were significantly correlated with the timely vaccination rate of HepB1 (P<0.05); Multivariate analysis indicated that low birth weight (OR=3.182, 95%CI: 2.129~4.756) and birth in home and other places except hospital (OR=4.691, 95%CI: 2.824~7.794) were the factors associated with of the timely vaccination rate of HepB1. Conclusions The vaccination rate of HepB1 is high in the investigated areas, while the timely vaccination rate of HepB1 is relatively low. Improving the hospital delivery rate and strengthening the correct understanding of contraindications for hepatitis B vaccination are the key to improve the timely vaccination rate of HepB1.