Coupled defect modes of photonic crystals can be characterized by the transmission spectrum shape that is closely linked to the stripe waveguide connecting the defects. Unlike the direct coupling cases where the phase shift of lightwave depends only on the defect mode frequency, we found that for the waveguide coupling cases the waveguide length and the dispersion relation must be also considered. By changing the waveguide length, the spectrum can exhibit periodically three-peak appearance, two-peak appearance, and flat top appearance. At frequencies close to the defect mode, the results of the coupled mode theory are in good agreement with the simulations using the finite-difference time-domain technique, verifying the validity of the theoretical model even in the complicated cases.