Water inrush is a common disaster in submarine mining. The key to preventing this disaster is to restrict the water‐conducting fissure propagation induced by mining from forming a flow channel to communicate with the overlying aquifer. The mechanical behavior of hydraulic fractures under stress disturbance lies at the heart of the problem. Hence, the multiple parallel bond—grain‐based model (multi Pb‐GBM) is introduced to explore the hydraulic fracture evolution law of crystalline granite under the influence of stress disturbance. The results show that: hydraulic fracturing under stress disturbance is clearly affected by the stress wave frequency; the higher the frequency is, the more difficult it is to crack, but the crack propagation speed is faster after crack initiation; the propagation direction of a crack is deflected towards the propagation direction of the stress wave and the crack dip angle is controlled by the maximum principal stress; the internal crystal boundary of the same mineral is the most stable one among the three contacts, the contact boundary between different minerals being the most fragile one. This research not only has a practical application value to seabed mining engineering, but also has important theoretical significance in enriching deep rock mechanics theory.