The trial production of natural gas hydrate reservoirs remains poor. Reasonable reservoir reconstruction, which can improve formation permeability, is an important approach to increasing the efficiency and enhancing production. In this work, water jet slotting is proposed to reconstruct an natural gas hydrate reservoir near a wellbore. The spatial slots formed by water jet slotting not only directly constitute high-permeability channels, but also generate disturbances to the surrounding in-situ sediment. Water jet slotting disturbances to nearby sediment was investigated using a three dimensional flow-structure coupling model to evaluate the proposed reconstruction method. The reservoir at the SH2 site in the Shenhu area of the South China Sea was used as the reference. A horizontal slotting arrangement along the vertical well was adopted. The results demonstrate that water jet slotting can change the primary stress state of the sediment around the wellbore, and generate a dominant stress relaxation zone and small stress concentration zone. Within the stress relaxation zone, the in-situ compressive stress was remarkably reduced or even transformed into tensile stress, accompanied by sediment displacement and volumetric expansion strain. This is conducive to loosening the sediment around the wellbore and improving the permeability characteristics. In addition, the influence of the water jet slotting parameters including slot radius, spacing, and number on disturbances to the nearby sediment was studied. Reservoir responses to water jet slotting under balanced and unbalanced bottom-hole pressures were compared and analyzed. This study provides a reference for natural gas hydrate reservoir reconstruction using water jet slotting.