Polymer solution for oil displacement is mostly used in the middle and late stage of water flooding reservoir development, and reservoir groundwater conditions are often one of the main conditions restricting polymer application. Therefore, it is necessary to develop salt tolerance of polymer solutions with different aggregation behaviors, so as to facilitate the synthesis and optimization of suitable polymer systems. The differences in the micro‐aggregation behavior of three polymers with different molecular structures were explored. On this basis, the effects of divalent metal cations on the properties of the polymer solutions were analyzed by assessing the micro‐aggregation behavior, apparent viscosity, hydrodynamic size, and shear rheological characteristics. The results showed that the linear partially hydrolyzed polyacrylamide (HPAM) was seriously affected by divalent cations, and the viscosity decreased obviously. The aggregation behavior of the polymer changed by hydrophobic association can enhance the salt tolerance of the solution. The hydrophobically modified partially hydrolyzed polyacrylamide (HMPAM) with “chain beam” aggregation behavior has strong intermolecular connection, which enables it to withstand the content of calcium and magnesium ions of 1100 mg l−1. When the content of calcium and magnesium ions exceeds 600 mg l−1, dendritic hydrophobically associating polymer (DHAP) will destroy the interaction between molecular chains, resulting in the decrease of apparent viscosity and hydrodynamic size. For polymer flooding in high‐salinity reservoir, salt tolerant polymer system can be constructed by optimizing molecular weight and hydrophobic group content.