The establishment of an isolation layer in submarine mining has long presented an enduring challenge. In the context of this research, we conducted a similarity simulation test to preliminarily ascertain the interplay between the thickness and extent of the isolation layer. Subsequently, we introduce an innovative approach that integrates fractal theory and the bonded block model (BBM) to simulate undersea isolation layer mining. The validation of this method hinges on on-site borehole scanning and displacement monitoring, which serve to depict the intricate fractal evolution of fractures and predict the optimal thickness of the isolation layer. Our findings affirm the robustness and validity of this method. Evaluation of the fractal dimensions of fractures reveals that a critical threshold of 1.7 exists to prevent structural failure of the isolation layer, while a limit of 1.5 is necessary to avert significant water ingress. Remarkably, the correlation dimension of the settlement time series closely aligns with the fractal dimension of the fractures, underscoring the feasibility of ensuring the safety of isolation layer mining through real-time settlement monitoring.