Specific emitter identification can detect emitters automatically by extracting and analyzing features. A novel specific emitter identification method based on 3D-Hilbert energy spectrum-based multiscale segmentation (3D-HESMS) is proposed. First, the time-frequency energy spectrum is derived via the Hilbert-Huang transform, that is, a complicated curved surface in a 3D space, namely, the 3D-Hilbert energy spectrum. The differential box dimension, multifractal dimension, lacunarity change rate, and 3D-Hilbert energy entropy are extracted to compose the feature vector under multiscale segmentation using fractal theory. Subsequently, communication emitter individual identification is obtained using the 4 features. Finally, the performance and complexity of the 3D-HESMS method are compared with those of 2 existing methods. Experiments show that the performance of the 3D-HESMS method is better than those of the 2 other methods. The extracted features with high stability, sufficiency, and identifiability can overcome the negative effects of the changes in signal-to-noise ratio and the number of training samples.