The finite element method (FEM) is widely used in engineering. However, it requires meshes to match discontinuities, which can complicate the pre-processing for problems with complex geometric domains. To overcome this limitation, numerous numerical methods have been developed and achieved, such as extended and generalized finite element methods (XFEM/GFEM), and numerical manifold method (NMM). However, ill-conditioning can reduce the stability of the solution and decrease the computing efficiency, which impedes the implementation of the above methods. Two sources of ill-conditioning have been researched and identified: the small cut ratios and the linear dependence from enrichment functions. Several modifications have been proposed, but they more or less have several problems or are limited in some cases. To address both issues simultaneously, a preconditioner is adopted in this study for complicated crack propagation problems. Numerical results demonstrate that the preconditioner can effectively and stably reduce the condition number and improve computational efficiency. Moreover, it has no impact on the crack propagation path and can be easily combined with the existing procedure.