Seawater intrusion has become a serious natural disaster in coastal regions around the world. Four shallow groundwater aquifers of Pearl River were sampled to study the changes of groundwater types and microbial communities caused by seawater intrusion. Seawater intrusion caused significantly increased cations (Na+, K+, Ca2+, Mg2+) and anions (Cl-, SO42-, HCO3-), and the groundwater type turned from HCO3-Ca to Cl•HCO3-Na•Ca and Cl•SO4-Na•Mg. The composition and diversity of groundwater geochemistry changes. Gammaproteobacteria species and Alphaproteobacteria species are dominant species, and the salinity of groundwater is the main environment factor that affect the relative abundance. The α-diversity of microbial community in three types groundwater are significantly different (P = 0.002，R2 = 0.959). The correlation between species in class level with different ions were also observed. Aeromonadales, Vibrionales, Alteromonadales and Oceanospirillales have a significant positive correlation with Cl-, SO42-, Na+ and Mg2+ (P < 0.05) in Cl•SO4-Na•Mg type, while in Cl•HCO3-Na•Ca type groundwater, Vibrionales and Oceanospirillales have positive correlations with Cl-, Na+, Ca2+, but negative correlations with HCO3-. Aeromonadales and Alteromonadales are opposite of this. The results demonstrate that groundwater type is the main factors influence the correlation between species and environments, other geophysical factors have weak influence. This shift of shallow groundwater type and microbial community under seawater intrusion were studied for the first time, it is momentous for forward exploration of groundwater microbial ecology in the coastal area under the background of seawater intrusion.