Background: As no population-based studies of group B Streptococcus (GBS) colonization rates in late pregnancy (at 35–37 weeks of gestation) have been conducted in China, the incidence of and risk factors for neonatal early-onset GBS disease (GBS-EOD) in China remains poorly understood. Objectives: To determine the GBS colonization rate in late pregnancy and neonatal GBS infection in Xiamen, China, and to assess the effectiveness of intrapartum antibiotic prophylaxis (IAP) for the prevention of neonatal GBS-EOD. Methods: A total of 49,908 pregnant women were enrolled between April 1, 2014 and March 31, 2017. Bacterial culture was used to diagnose GBS infection in both pregnant women and neonates. Women with GBS colonization received IAP during parturition or rupture of fetal membranes. Results: The GBS colonization rate was 13.89% (6,933/49,908); 50,772 neonates were born to 49,908 pregnant women, of whom 75 (1.48 per 1,000) were diagnosed with GBS-EOD. The incidence of GBS-EOD among neonates born to GBS-positive mothers (8.77‰; 62/7,068) was 29 times higher than that of neonates born to GBS-negative mothers (0.30‰; 13/43,704). Logistic regression analysis indicated that gestational bacteriuria, GBS disease in infants from previous pregnancies, and chorioamnionitis were risk factors for GBS-EOD (p = 0.007, p = 0.000, and p = 0.018, respectively). IAP effectively protected against neonatal GBS-EOD (p = 0.011). Conclusions: GBS colonization was detected in nearly 14% of late pregnant women. The IAP for reducing GBS-EOD was effective. Therefore, universal screening of maternal GBS and subsequent IAP for those with GBS colonization should be implemented in China.