To investigate the molecular properties and microscopic aggregation of asphaltenes and the microcosmic mechanism of asphaltene deposition，we adopt molecular dynamics methods to establish the average molecular configuration of representative asphaltenes. It can be utilized to construct the initial configuration of the asphaltene simulation system to simulate the migration of asphaltenes in the formation rock. The simulation experiment results indicate the radial distribution of asphaltenes，as typical amorphous matter，are generally in the pattern of short-range order and long-range disorder.In addition，simulated annealing optimization can fully release stress from the molecular structure，which is conducive to reducing its energy ground state. As the distance between molecules increases，the Van der Waals interaction between the molecules becomes weak，but the electrostatic interaction becomes dominant among non-bonding interactions of the system.It can be observed from the final migration state of the asphaltene simulation system that the main body of aromatic nucleus and part of the aliphatic chain of the asphaltene molecules tend to be gradually adsorbed to the surface of the silica molecular layer，altering the wettability of the rock surface from hydrophilic to lipophilic. The π-π stacking of the aromatic nucleus drives the asphaltene molecules to aggregate，leading to the flocculation and deposition of asphaltenes from crude oil.Wettability alteration and the pore-throat blockage of rock are important mechanisms for the reduction of oil recovery caused by asphaltene deposition.