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Under the guidance of molecular simulation technology, the Monte Carlo molecular mechanics simulation was used to calculate the compatibility of different lipophilic groups with each component of bitumen, and the compatibility of different hydrophilic groups with water. Based on the calculated results of interaction parameters Chi and mixture energy Emix, the preferred structures of lipophilic and hydrophilic groups of bitumen emulsifier were determined. The target bitumen emulsifier was then synthesized by the reaction of organic acid and polyamine. The molecular simulation results showed that the compatibility of lipophilic group T11 with the bitumen was the best, and the mixing ability of the hydrophilic group H5 with water was excellent. The experimental results show that the preferred structures T11H5 had a good emulsifying performance to prepare emulsified bitumen with good storage stability, consistent with the results of the molecular simulation.