Objective To study the trend of the mortality rate and the leading causes of death among children under 5 years of age in Shenzhen, China, from 2003 to 2013. Methods The surveillance data of mortality among children under 5 years of age in Shenzhen from 2003 to 2013 were collected, and the mortality rates among infants (IMR) and children under 5 years of age (U5MR) with different household types and the leading causes of death were determined. Results Between 2003 and 2013 the IMR and U5MR in Shenzhen dropped by 61.56% and 60.56%, respectively from 7.83‰ and 10.04‰ in 2003 to 3.01‰ and 3.96‰ in 2013. The IMR and U5MR of the non-household population were significantly higher than those of the household population. The leading causes of death among children under 5 years of age were preterm birth/low birth weight, congenital heart disease, accidental asphyxia, septicemia, and birth asphyxia. Conclusions The U5MR has substantially reduced in Shenzhen. To further reduce the U5MR, it is important to improve prenatal diagnosis and neonatal resuscitation, enhance perinatal health care and accident prevention, and strengthen health care of floating population.