If the fault sources can be located in a timely and accurate manner when an unmanned aerial vehicle (UAV) has an early minor fault, a major accident can be avoided. In light of the early fault of the six-rotor UAV motors, this paper proposes a fusion fault diagnosis model based on Conformal Fourier Transform (CFT) and the improved Self-Organizing Feature Map (SOM) neural network. Firstly, to overcome the weakening of UAV fault information caused by external interference and solve the problem that the non-uniform distribution of the collected flight data affects the accuracy of the frequency domain processing, on the basis of changing the processing method of the Fourier integral kernel and using high-order numerical integration, an improved Conformal Fourier Transform (CFT) algorithm optimized by spectrum refinement strategy is proposed. Then this algorithm is used to further intensify the main features and build a clear fault state in a cycle processing method. Secondly, an improved SOM neural network is designed. We use the unweighted average distance (UPGMA) of the agglomerative hierarchical clustering algorithm to detect the clustering areas of each pattern category of the data samples, and the weight vectors of different clustering areas are used to randomly initialize the connection weights of SOM network, thereby improving the clustering speed and convergence effect. On this basis, CFT algorithm is integrated into the improved SOM network to realize the multi-module collaboration strategy and finally form a new fusion fault diagnosis model. INDEX TERMS CFT algorithm, improved SOM network, main feature intensification, hierarchical clustering, fault diagnosis.