This paper analyzed the excess mortality change in nine districts of Nanjing city, based on mortality data and meteorological data from 2004 to 2010. Taken a typical heat waves process in summer of 2006 as an example, it was discussed of the effect of the heat process on different gender, different age groups , and various disease death toll and excess mortality changes. The excess mortality was associated with the average maximum temperature and average minimum temperature during the heat waves. Excess mortality occurred in the middle of June heat wave when excess mortality was much higher than in other time periods. In late June, early July to early August, the excess mortality is relatively small. The average daily deaths are increasing with increasing age for male and female, and every age death numbers is higher than that with no heat waves during the heat wave period. In addition to the respiratory system diseases, diseases of the genitourinary system, other diseases, residual disease in the heat waves has increased, and diseases of the nervous system and the endocrine system diseases of excess mortality rate reached a staggering 342.93% and 119.63%, accounting for almost half of the total heat excess mortality. The heat waves effect is very obvious. The conclusion is of great significance for prevention of high temperature heat harm.