Hydraulic fracturing is widely applied to economic gas production from shale reservoirs, but the effect of the shale mineral composition on the physical-chemical reactions during hydraulic fracturing is still poorly understood. To develop a foundational understanding of chemical interactions occurring on shale with different mineralogical compositions, two different types of mineral composition marine shale (carbonate-poor and carbonate-rich) from the Niutitang Formation were reacted with slick water fracturing fluid in a laboratory reactor at 100°C and 50 MPa for three days. To identify the changes of the pore structure characteristics during hydraulic fracturing, the field emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), low-temperature nitrogen adsorption, and porosity measurement were performed on the original and treated shale samples. After the slick water treatment, the dissolution of pyrite in carbonate-poor shale (obtained from Youyang County, labeled as YY) was observed by FE-SEM and XRD analyses, while in carbonate-rich shale (obtained from Guzhang County, labeled as GZ), the carbonate dissolution was observed. Results from the low-temperature N2 adsorption and porosity measurement demonstrated that the variation trend of pore structure characteristics for the YY and GZ shale samples was quite different after reacting with slick water fracturing fluid. For YY shale, the specific surface area, total pore volume, and porosity increased after the reaction, whereas an opposite trend was observed in the GZ shale. Moreover, the fractal dimension analysis illustrated that the pore surface became less rough and the pore structure became more complex in the YY shale, whereas the degree of pore surface roughness and pore structure complexity of the GZ shale was reduced. The results demonstrated that the initial mineralogical composition of shale played an important role in pore structure alteration during hydraulic fracturing.