Investigating mechanisms and characteristics of the non-tectonic deformation has crucial implications for evaluating the subsurface stress evolution. In this study, we continuously tracked the seasonal velocity changes of Rayleigh wave at 2–10 s with the ambient noise interferometry and discrete wavelet decomposition, in different regions along the actively deforming North–South Seismic Belt (NSSB) and the stable Guangdong region in the South China block in China. The seasonal velocity changes exhibit strong lateral variations across different regions, with much larger seasonality (annual periodicity) and amplitude along the NSSB than those in the stable Guangdong region. There are also small-scale lateral variations inside of each region and generally larger amplitudes of the seasonal velocity changes at greater depth, but the phases (peaks, mostly in winter or summer) at different depths are consistent. The mechanism of the seasonal changes is most likely the direct loading effect of the precipitation, as indicated by consistency in their phases. However, the amplitudes of the seasonal velocity changes seem not controlled by the amount of precipitation, but are more dependent on the tectonic deformation at the different scales, from the correlation between the amplitude of the velocity change and the absolute strain rate. We demonstrate that the crustal media in the regions with larger tectonic background stress are more sensitive to the seasonal loadings. The new finding also highlights the role of the external seasonal loadings in the modulation of seismic activities and risk evaluations. Keypoints•Seasonal seismic velocity variations are found in different regions in China, likely from direct hydrological loadings of precipitation.•The spatial pattern of the seasonal velocity changes is consistent with the distribution of tectonic deformation at multi-scales.•The amplitude of the seasonal velocity changes is more dependent on the magnitude of local deformation than the amount of precipitation.