Objective To examine the association between epidemiological characteristics of hemorrhagic fever with renal syndrome (HFRS) and meteorological factors in Shenzhen City during the period from 2012 to 2019. Methods Average atmospheric pressure, average air temperature, average relative humidity, precipitation, wind speed, and sunshine duration were captured from Meteorological Bureau of Shenzhen City each month from 2012 to 2019. The average monthly rodent densities in Shenzhen City from 2012 to 2019 were acquired from the Vector Surveillance Management System of Guangdong Provincial Center for Disease Control and Prevention, and the monthly HFRS incidence was retrieved from Shenzhen Municipal Disease Surveillance System from 2012 to 2019. The correlation between meteorological factors and the monthly incidence of HFRS was examined us ing Spearman’s rank correlation in Shenzhen City, and the temporal trends in monthly HFRS incidence and the degrees of freedom for the rodent density were determined in Shenzhen City with a generalized additive model. The optimal lag time was identified using excess risk (ER) and its 95% confidence interval (CI), and univariate and multivariate models were fitted to evaluate the impact of meteorological factors on HFRS incidence in Shenzhen City. Results The median number of incident HFRS cases was 3.00 (interquartile range, 3.25) in Shenzhen City from 2012 to 2019, with an average air temperature of (23.44 ± 4.91) °C, average relative humidity of (76.05 ± 7.61)%, median precipitation of 4.10 (interquartile range, 6.83) mm, average wind speed of (1.97 ± 0.26) m/s, average sunshine duration of (5.17 ± 1.64) h, and median monthly rodent density of 1.74% (interquartile range, 2.52%). Spearman’s rank correlation analysis showed that the average air temperature positively correlated with average relative humidity (r_s = 0.420, P < 0.05), precipitation (r_s = 0.658, P < 0.05) and sunshine duration (r_s = 0.633, P < 0.05), and the atmospheric pressure negatively correlated with average air temperature (r_s = −0.925, P < 0.05), relative humidity (r_s = −0.614, P < 0.05), precipitation (r_s = −0.789, P < 0.05) and sunshine duration (r_s = −0.437, P < 0.05), while the average relative humidity correlated positively with precipitation (r_s = 0.724, P < 0.05) and negatively with sunshine duration (r_s = −0.218, P < 0.05). Univariate modeling analysis showed that the ERs and their 95% CI were 0.639% (0.540%, 0.737%) for average atmospheric pressure, −7.157% (−8.113%, −6.190%) for average air temperature, −3.603% (−4.219%, −2.985%) for average relative humidity, −5.889% (−7.085%, −4.669%) forprecipitation,21.881% (−5.149%, 56.612%) for average wind speed, and −13.877% (−16.641%, −11.022%) for sunshine duation (all P values < 0.05). Multivariate modeling analysis showed that in the ensemble model combining average atmospheric pressure and precipitation, the highest ER (6.686%) was caused by increased average atmospheric pressure, and the highest absolute ER values for average air temperature (6.615%), average relative humidity (3.107%) and precipitation (5.386%) were seen after adjustment only for sunshine duration (all P values < 0.05), while the highest absolute ER for sunshine duration (11.875%) was found after adjustment for precipitation (P < 0.05). Conclusions An increase in average air temperature, relative humidity, precipitation and sunshine duration resulted in a reduced incidence rate of HFRS in Shenzhen City from 2012 to 2019, and an increase in average atmospheric pressure increased the incidence of HFRS. Meteorological factors are important determinants affecting HFRS incidence in Shenzhen City.