Shale gas has enormous potential and has become a hotspot in recent decades. To exploit shale gas, a variety of working fluids (drilling fluid, fracturing fluid, etc.) have to be applied in drilling and well-completion engineering. When fluid contacts with shale, spontaneous imbibition occurs, affecting wellbore stability, fracturing fluid loss, and shale gas production. In the past few years, numerous researchers conducted studies on shale spontaneous imbibition, yet the vast majority of their works are derived from conventional method based on sandstone and carbonate. One of the characteristics of shale is strong hydration, which has been widely reported. During the interaction between liquid and shale, spontaneous imbibition is accompanied by hydration. Shale hydration mainly involves two aspects, i.e., osmotic pressure and hydration structural damage. Now there is still no research on studying the hydration effect during spontaneous imbibition, and how hydration affects spontaneous imbibition is still not fully understood. Therefore, in this paper, considering osmotic pressure and hydration structural damage, spontaneous imbibition in shale formation has been investigated. Besides, according to the Hagen−Poiseuille law, a novel analytical model has been established by coupling imbibition and hydration. In comparison to experimental data of spontaneous imbibition, practicability of this spontaneous imbibition model has been verified. On the basis of this new model and spontaneous imbibition test, influences of salinity and hydration on shale spontaneous imbibition have been systematically discussed. Results indicate that salinity reduces spontaneous imbibition by lowering the driving force of imbibition and restricting hydration damage. Hydration structural damage is its major influencing mechanism for shale spontaneous imbibition. In the shale exploitation, this model can offer guidance for evaluating fracturing fluid loss and hydration damage, which are practical for drilling and hydraulic fracturing design. Besides, the outcome of this paper is beneficial for improving our understanding on spontaneous imbibition in shale formation.