Previous studies have reported that temperature is the main meteorological factor associated with influenza activity. This study used generalized additive models (GAMs) to explore the relationship between temperature and influenza activity in China. From the national perspective, the average temperature (AT) had an approximately negative linear correlation with the incidence of influenza, as well as a positive rate of influenza H1N1 virus (A/H1N1). Every degree that the monthly AT rose, the influenza cases decreased by 2.49% (95%CI: 1.24%-3.72%). The risk of influenza cases reached a peak at -5.35 °C with RRs of 2.14 (95%CI: 1.38-3.33) and the monthly AT in the range of -5.35 °C to 18.31 °C had significant effects on the incidence of influenza. Every degree that the weekly AT rose, the positive rate of A/H1N1 decreased by 5.28% (95%CI: 0.35%-9.96%). The risk of A/H1N1 reached a peak at -3.14 °C with RRs of 4.88 (95%CI: 1.01-23.75) and the weekly AT in the range of -3.14 °C to 17.25 °C had significant effects on the incidence of influenza. Our study found that AT is negatively associated with influenza activity, especially for A/H1N1. These findings indicate that temperature could be integrated into the current influenza surveillance system to develop early warning systems to better predict and prepare for the risks of influenza.