Brushless direct current (BLDC) motors are the source of flight power during the operation of rotary-wing unmanned aerial vehicles (UAVs), and their working state directly affects the safety of the whole system. To predict and avoid motor faults, it is necessary to accurately understand the health degradation process of the motor before any fault occurs. However, in actual working conditions, due to the aerodynamic environmental conditions of the aircraft flight, the background noise components of the vibration signals characterizing the running state of the motor are complex and severely coupled, making it difficult for the weak degradation characteristics to be clearly reflected. To address these problems, a weak degradation characteristic extraction method based on variational mode decomposition (VMD) and Laplacian Eigenmaps (LE) was proposed in this study to precisely identify the degradation information in system health data, avoid the loss of critical information and the interference of redundant information, and to optimize the description of a motor’s degradation process despite the presence of complex background noise. A validation experiment was conducted on a specific type of motor under operation with load, to obtain the degradation characteristics of multiple types of vibration signals, and to test the proposed method. The results proved that this method can improve the stability and accuracy of predicting motor health, thereby helping to predict the degradation state and to optimize the maintenance strategies.