In order to solve the problem of fracture caused by the failure of the native defects of wind turbine blades, the mechanism of crack initiation is defined by analyzing the quantitative relation of energy release during the transition from mesoscopic defects to macroscopic cracks under external loading. Firstly, a new stress function is constructed according to the load characteristics of wind turbine blade. Based on the basic formula of the orthotropic composite, the stress intensity factor, the stress strain and the displacement of the native defect are calculated, and the plastic strain energy of the mesoscopic defects can be obtained. Using the infrared thermal imager, the temperature field of transition process of native defects is collected and the thermal energy dissipation is calculated. Then, based on the irreversible thermodynamics, the variation law of the internal storage energy with the fatigue cycles is obtained. Finally, the blade specimen with bubble and fiber fracture is selected for the fatigue test. The results show that the error between the calculated displacement using the new stress function and the test value is smaller. This indicates that the proposed stress function can be applied to calculate the plastic strain energy for the mesoscopic defects. When the native defects are transitioned into a small crack, the change of the internal energy storage can be used as to determine the type and extent of the defects. The fatigue energy theory of multilayer composites is explored in this study, which helps to realize the life cycle monitoring of key components of wind turbine.