Hydraulic fracturing is an important technique to develop deep shale gas. After hydraulic fracturing, a large amount of fracturing fluid fails to flow back and retains in deep shales. This phenomenon leads to fracturing fluid imbibition and significantly impacts on gas production. However, the understanding of imbibition mechanism in deep shales is very limited. In this work, the microscopic mechanism of fracturing fluid imbibition into illite pores of deep shales was studied using molecular simulation. The factors affecting imbibition were also analyzed. Results show that water imbibition in illite pores can be divided into three stages. In stage 1, the hydrogen bonds between water molecules and illite pore walls are formed, which forces water to enter the pores and becomes a water layer. In stage 2, the hydrogen bonds between water molecules and the water layer are formed, and gas begins to be displaced out of the pores by water. In stage 3, water molecules no longer enter the pores, and the system becomes equilibrium. As for the influencing factors, fugacity pressure mainly affects the imbibition time. The imbibition time becomes longer when fugacity pressure rises. Pore size plays a significant role in imbibition. Gas in illite pores can be totally displaced if the pore size is smaller than 5 nm. The imbibition is also affected by the amount of water. More gas tends to be displaced out of the pores when the ratio of water volume to pore volume (RWP) increases.