Objectives. This study aims to analyze the cesarean section (CS) rates and vaginal delivery rates in tertiary hospitals of China, explore the costs of two different deliveries, and examine the relative influencing factors of the costs in both CS and vaginal deliveries. Methods. 30,168 anonymized obstetric medical cases were selected from three sample tertiary hospitals in Chongqing Municipality from 2011 to 2013. Chi-square test was used to compare the distributions of CS and vaginal deliveries under different indicators. Mann-Whitney test and Kruskal-Wallis test were adopted to analyze the differences under different items. Multiple linear regression was used to determine the influencing factors of the costs of different delivery modes. Results. (1) The rates of CS were 69%, 65.5%, and 59.2% in the three sample tertiary hospitals in Chongqing from 2011 to 2013. (2) The costs and the length of stay of CS were greater than those of vaginal delivery, which had significant differences (P < 0.005). (3) The areas, length of stay, age, medical insurance, and modes of delivery were the influencing factors of both CS and vaginal delivery costs. Discussion. The high CS rates in China must be paid significant attention. The indicators of two modes of delivery should be regulated strictly. CS rate reduction and saving medical resources will be the benefits if vaginal delivery is chosen by pregnant women.