As an effective means to manipulate elastic wave energy, the defect mode of phononic crystals (PCs) has recently been employed to implement vibration energy harvesting by localizing waves within certain areas at defect frequencies. Prior research has indicated that the thermal environment affects the defect behavior and energy harvesting of single defects. However, the dynamic characteristics of multi-defect phononic crystals have not yet been discussed. This paper presents an investigation of the coupling behavior and energy harvesting of double defects in heated PC beams. The frequencies and mode shapes of defect modes are studied for different defect pairs within the first bandgap. Results indicate that the difference in the single-defect frequency between the two defects plays a dominant role in determining the intensity of the defect interaction which splits the defect modes. Meanwhile, the influence of the energy distribution around the defects on the coupling behavior becomes prominent when the two defects are quite close to each other. These two factors could cause degeneration of the defect modes. As an external factor, thermal load could enhance the defect coupling intensity, and may reactivate the degenerated defect modes. This effect would increase as the initial defect interaction gets stronger. For vibration energy harvesting, temperature rise may lead to a significant reduction in defect-based harvested energy, even though the number of defect-induced resonance peaks could be increased in the thermal environment. The thermosensitivity of harvesting performance varies greatly for different combinations of defects. Thermal effects should be considered in the design of defect-based harvesters.