In Shengli oilfield，the reservoir heterogeneity is intensified in the extra-high water-cut period，so the effective control system must be used to realize the deep control of the formation. The field test of the existing control system SP-01 in the Gudong test area failed to achieve the expected effect，so it is urgent to conduct research on the molecular structure optimization and improvement of the existing control system. Traditional manual design is time-consuming and costly in the synthesis and verification methods. In this paper，the regulation mechanism was furtherly understanded using the computer molecular simulation method，the relationship between the molecular structure of polymer and the fluid mechanics volume or intermolecular interaction energy was studied and the optimal molecular structure was obtained. Moreover，the polymer NSP-02 was synthesized according to the optimal simulated results，and the viscosity-increasing ability of the new synthetic polymer NSP-02 was compared with that of SP-01. The molecular simulation results showed that it was not a simple linear relationship between the molecular structure of polymer and the fluid mechanics volume or intermolecular interaction energy. The optimal molecular structure of polymer should be determined according to the change of the polymer molecular weight，the hydrophobic carbon chain length and micro block length. The molecular weight and viscosity-increasing ability of the new synthetic polymer NSP-02 in the laboratory were both stronger than that of the polymer SP-01. The indoor experimental verification results are consistent with the computer molecular simulation results，so the computer molecular simulation can be faster and more effective to guide artificial synthesis.