Electromagnetically induced transparency-like (EIT-like) effect is a promising research area for applications of slow light, sensing and metamaterials. The EIT-like effect is generally formed by the destructive interference of bright-dark mode coupling and bright-bright mode coupling. There are seldom reports about EIT-like effect realized by the coupling of two dark modes. In this paper, we numerically and theoretically demonstrated that the EIT-like effect is achieved through dark-dark mode coupling of two waveguide resonances in a compound nanosystem with metal grating and multilayer structure. If we introduce |1〉, | 2 〉 and | 3 〉 to represent the surface plasmon polaritons (SPPs) resonance, waveguide resonance in layer 2, and waveguide resonance in layer 4, the destructive interference occurs between two pathways of | 0 〉 → | 1 〉 → | 2 〉 and | 0 〉 → | 1 〉 → | 2 〉 → | 3 〉 → | 2 〉 , where | 0 〉 is the ground state without excitation. Our work will stimulate more studies on EIT-like effect with dark-dark mode coupling in other systems.