Water uptake induced by fluid–rock interaction plays a significant role in the recovery of flowback water during hydraulic fracturing. However, the existing accounts fail to fully acknowledge the significance of shale anisotropy on water uptake typically under in situ reservoir temperature. Thus we investigated the shale-hydration anisotropy using two sets of shale samples from the Longmaxi Formation in Sichuan Basin, China, which are designated to imbibe water parallel and perpendicular to shale bedding planes. All the samples were immersed in distilled water for one to five days at 80 °C or 120 °C. Furthermore, samples’ topographical and elemental variations before and after hydration were quantified using energy-dispersive spectroscopy–field-emission scanning electron microscopy. Our results show that shale anisotropy and imbibition time strongly affect the width of pre-existing micro-fracture in hydrated samples. For imbibition parallel to lamination, the width of pre-existing micro-fracture initially decreases and leads to crack-healing. Subsequently, the crack surfaces slightly collapse and the micro-fracture width is enlarged. In contrast, imbibition perpendicular to lamination does not generate new micro-fracture. Our results imply that during the flowback process of hydraulic fracturing fluid, the shale permeability parallel to bedding planes likely decreases first then increases, thereby promoting the water uptake.