In order to study hydrogeochemical effect in the process of seawater intrusion (SI), and provide scientific basis for comprehensive management of water resources and water ecological restoration, the Longkou city of Shandong province in China was taken as an example in this study. Based on the observed data, traditional hydrogeochemistry methods of hydrochemistry analysis, correlation analysis, principal component analysis, and reverse geochemical simulation was firstly comprehensively combined with stable isotope tracing in Longkou city, and this is the first study to use the isotope method to study SI in the study area. The results showed Cl− had high correlation with Na+, Mg2+, and K+. The hydrochemical types of groundwater in Longkou city were mainly HCO3.Cl-Na.Ca, and HCO3.Cl-Ca, showing the evolution of HCO3-Ca to HCO3.Cl-Na to Cl-Na from the inland to the coastline. Stable isotopes analysis with δ2H, δ18O and 87Sr/86Sr indicated the main source of groundwater was atmospheric precipitation. The SI degree was the strongest at the junction of the west and north coast zones, with high values of δ2H and δ18O. The high Sr2+ concentration of groundwater was mainly from SI and groundwater–rock interactions. In the SI process, the mixing of seawater and fresh water took place first, and then different degrees of cation exchange and mineral dissolution and sedimentation occurred. Results of reverse hydrogeochemical simulation showed dolomite and quartz precipitated, with negative migrated masses of 1.38 × 10−3 and 1.08 × 10−5 mol/L on simulation Path 1, respectively, where calcite, halite, and gypsum dissolved with positive migrated masses of 2.89 × 10−3, 3.52 × 10−3, and 4.66 × 10−4 mol/L, respectively, while dolomite and gypsum precipitated and calcite, halite, and quartz dissolved on simulation Path 2. On simulation Path 3, the dolomite, gypsum, halite, and quartz were dissolved, and calcite was precipitated, with a negative migrated mass of 1.77 × 10−4 mol/L.