Objective To understand the epidemiological characteristics of influenza and hand-foot-mouth disease in Ganzhou region and provide scientific basis for the prevention and treatment of influenza and hand-foot-mouth disease in this region. Methods The surveillance sample data of influenza and hand-foot-mouth disease cases reported by Ganzhou sentinel hospital from 2017 to 2021 were retrospectively analyzed. Throat swabs of patients were collected and detected by RT-PCR. The etiological and epidemiological statistics and analysis were carried out in combination with patient information. Results The percentage of influenza in 2020-2021 was significantly higher than that in the other three years, with the increased rate of 24.90%, 21.50% and 24.60% respectively（x²= 75.768, P < 0.05)., The number of throat swabs collected from 2020 to 2021 was increased significantly compared with the other three years, and the positive rate of pathogen detection was decreased significantly compared with the other three years, with 87.1%, 64.2% and 75.1%, respectively, with a significant decrease（ x²=381, P<0.01). The epidemic mainly broke out in winter and spring, and occasionally in summer. There was no outbreak of epidemic from January to December 2020, and the outbreak did not occur until the end of the winter (the next January). From 2020 to 2021, the average number of cases of different genders and ages was decreased to varying degrees, and the incidence of hand-foot-mouth disease in men was significantly higher than that in women, and the incidence of hand-foot-mouth disease in 1-3 years old was significantly higher than that in other ages (P < 0.05). The positive rate of pathogen detection of hand-foot-mouth disease in 2021 was significantly lower than that in other years（x²=74.589, P<0.01). From 2019 to 2021, the annual epidemic virus strains varied in varying degrees, and the proportion of CA6 virus strains was increased year by year; the proportion of CA16 virus strains was increased from 2019 to 2020 and decreased significantly from 2020 to 2021, accounting for only 2.13%. Conclusion The incidence of influenza in Ganzhou from 2017 to 2021 has obvious seasonality, mainly concentrated in winter and spring and the concentrated epidemic is mainly in schools. In the same period, the risk of HFMD in Ganzhou was higher in men than in women, mainly in children aged 1-3 and the dominant strain was CA16.