We apply the multiscale basis functions for the singularly perturbed reaction-diffusion problem on adaptively graded meshes, which can provide a good balance between the numerical accuracy and computational cost. The multiscale space is built through standard finite element basis functions enriched with multiscale basis functions. The multiscale basis functions have abilities to capture originally perturbed information in the local problem, as a result our method is capable of reducing the boundary layer errors remarkably on graded meshes, where the layer-adapted meshes are generated by a given parameter. Through numerical experiments we demonstrate that the multiscale method can acquire second order convergence in the L2 norm and first order convergence in the energy norm on graded meshes, which is independent of ɛ. In contrast with the conventional methods, our method is much more accurate and effective.