Recent global influenza resurgences, escalating to pandemics, emphasize the urgency for effective vaccinations. Despite their efficacy, vaccines offer limited protection against A/H3N2 variants. Thus, elucidating the spatial patterns and underlying drivers of A/H3N2 seasonality is critical for its management. However, the mechanisms governing this seasonality are not fully understood. The study conducted a collaborative and interdisciplinary analysis of influenza A/H3N2 epidemiology in China from 2012 to 2018, utilizing national influenza surveillance data, viral gene sequence data, and meteorological information. We initially examined the spatiotemporal distribution of influenza A/H3N2 across different temperate zones in China. Subsequently, we employed Bayesian “SkyGrid” reconstruction analysis to gain insights into the population dynamics of the influenza A/H3N2 virus within China´s temperature zones. Additionally, we utilized generalized additive models (GAM) to assess the influence of meteorological factors on the seasonal prevalence of influenza A/H3N2. Our analysis of China´s national influenza data revealed distinct seasonal patterns for A/H3N2: winter epidemics prevailed in temperate zones, while summer and autumn outbreaks occurred in subtropical and tropical areas. The seasonality of influenza A/H3N2 across China´s diverse climatic zones is shaped by the interplay of virus migration and meteorological factors. Virus migration introduced new variant populations during seasonal epidemics of influenza A/H3N2 to different temperature zones in China, thereby seeding subsequent seasonal outbreaks. Our findings also indicate that meteorological elements trigger influenza A/H3N2 activity following virus migration. Moreover, the spatial variations in influenza A/H3N2 seasonality in China can be attributed to specific temperature thresholds, approximately 1 °C and 24 °C. These thresholds could serve as potential indicators for A/H3N2 prevalence. This insight is invaluable for tailoring region-specific prevention and control strategies in China and other regions with similar environmental conditions.