Drowning is the leading cause of death for young people. For a long time, drowning mortality is much higher in southern China than in northern China. Climate of the two parts of China are quite different. The aim of this study is to explore relationship between precipitation, temperature in summer, water system distribution and higher mortality rate of drowning in southern China than in northern China. We collected geographical distribution of drowning mortality, precipitation, temperature, population density, water system and income of China. Statistical tests were performed to find if there are any statistical difference of drowning and its influencing factors between northern and southern China. We conducted a logistic regression to evaluate the association between drowning and climatic factors. Life expectancy lost caused by drowning in northern and southern China were calculated. Abundant water system and plenty precipitation (OR: 1.589, 95%CI: 1.350 ~ 1.871), hotter summer (OR: 1.252, 95%CI: 1.075 ~ 1.459) and longer summer (OR: 1.357, 95%CI: 1.161 ~ 1.585) in southern China leaded to significantly higher drowning compared with northern China, especially for children. Life expectancy lost caused by drowning in southern China in 1990 and 2013 was 0.492 and 0.162 year, respectively, while the data in northern China is 0.245 and 0.101 year, respectively. High temperature in summer and low economic performance in part of Xinjiang are key reasons for its high ranking in drowning mortality, despite the fact that Xinjiang is located in northern China. Climatic factors formed higher mortality of young people in southern China. Our findings suggest decision-makers of different region should take more adaptive and effective measures to reduce drowning risks.