Background Hand, foot and mouth disease (HFMD) is most frequently caused by several serotypes of human enterovirus (EV) including Enterovirus 71 (EV71), Coxsackievirus A16 (CV-A16) or other types of EV. Children under 5 years old are the most susceptible to HFMD. The aim of this study was to determine the epidemiological characteristics and the relationship between severe and mild HFMD. Methods We collected 4760 probable HFMD cases with skin papular or vesicular rashes on the hands, feet, mouth or buttocks in Hangzhou from 2016 to 2018. Specimens of these cases were collected and the pathogen of EV71, CV-A16, CV-A6, CV-A10, CV-A2 and CV-A5 was classified by RT-PCR. Then the pathogen distribution and clinical status of children with HFMD were described. Results From Jan. 1, 2016 to Dec. 31, 2018, the incidence and prevalence of HFMD were seasonal each year. Among the 4760 probable HFMD cases, 3559 cases were confirmed (74.8%, 3559/4760), including 426 cases of EV71 infections (8.9%, 426/4760, 249 cases of CV-A16 infections (5.2%, 249/4760) and 2884 cases of other enteroviruses infections (60.6%, 2884/4760). The percentage of EV positive HFMD cases with non-EV71 and non-CV-A16 was more than 80% (2884/3559), which increased year by year. The percentage of EV71 decreased year by year in the last three years especially in 2018. Among the 1297 cases randomly selected of other EV infections in 2017 and 2018, there were 835 (64.4%) cases of CV-A6 infections, 177 (13.6%) cases of CV-A10 infections, 100 (7.7%) cases of CV-A2 infections, 40 (3.1%) cases of CV-A5 infections, 3 (0.02%) cases of mixed infections and 11.0% untyped enteroviruses infections. Preschool children were still the primary population susceptible to HFMD, and the age of the children infected with other enteroviruses tended to be younger. In severe cases, EV71 infection was the main cause. Conclusions The other EV especially CV-A6 increased obviously and EV71 decreased obviously in the three years. Characterizing the epidemiology and the relationship between severe and common cases of HFMD would provide relevant evidences for the prevention and treatment of HFMD.