The variations in precipitation have displayed a complex pattern in different regions since the mid-to-late-Holocene. Cloud formation processes may have a significant impact on precipitation, especially during the tropical marine processes and summer monsoon which convey abundant water vapor to coastal southern China and inland areas. Here, we use two 7500 year sedimentary records from the Pearl River Delta and the closed Maar Lake, respectively, in coastal southern China to reconstruct the mid-to-late-Holocene humidity variability and explore its possible relationship with cloud cover modulated by the Earth’s magnetic fields (EMF). Our proxy records document an apparent increase in wetness in coastal southern China between 3.0 and 1.8 kyr BP. This apparent increase in humidity appears to be consistent with the lower virtual axial dipole moments and, in turn, with a lower EMF. This correlation suggests that the EMF might have been superimposed on the weakened monsoon to regulate the mid-to-late-Holocene hydroclimate in coastal southern China through the medium of galactic cosmic rays, aerosols, and cloud cover. However, further investigations are needed to verify this interaction.