A method for material fragmentation based on Lagrangian FEM with the concept of nodes separation is proposed. This method is consisted of nodes separation mechanism and elements distortion erosion. In the simulation the nodes of failure elements are separated to form crack and distorted elements are detected and eliminated to prevent singularity. Nodes separation method can greatly improve the energy loss disadvantage in the failure erosion method. Based on LS-dyna secondary development the method is implemented. Hypervelocity impact problem of satellite protective structure is simulated and compared to experimental data for calibration. The performance of multi layer aluminum mesh shield under hypervelocity impact is also evaluated. The results show the high efficiency and applicability of nodes separation method in practical problems.