Based on the waveguide-two-cavities-quantum-dot system’s Hamiltonian and Heisenberg equation of motion for system operators, the input-output relations of the optical modes were derived. Moreover, using the Green function theory, the coupling rate between the cavity and waveguide was analytically defined. Based on the above, the analytic solution of the transmission spectra was derived. By numerical calculation, the transmission spectra of the whole system were investigated with varying optical length (which induces the phase separation between the two cavities) and detuning factor between the two cavities. The results reveal that the transmission spectra are closely dependent on the distance and detuning of the two cavities. This structure has potential applications in quantum information, quantum computation and optical switch.