Early fatigue damage is an important factor affecting the service safety of 316L stainless steel parts formed by selective laser melting (SLM) technology. Nonlinear ultrasonic testing for early fatigue damage in SLM 316L stainless steel specimens was carried out. A new method for evaluation of early fatigue damage based on nonlinear ultrasonic testing was proposed. Empirical mode decomposition (EMD) was applied to the unsteady ultrasonic testing signal, and the signal was decomposed into multiple intrinsic mode functions (IMFs) that meet certain conditions; then, the specific IMF (ESI) containing the effective fatigue damage information was extracted. Lastly, fast Fourier transform (FFT) was applied to the specific IMF signal to obtain the required information to evaluate the damage in the measured part caused by fatigue. The results of nonlinear ultrasonic testing agreed well with transmission electron microscope experimental analysis and theoretical model of acoustic nonlinearity caused by dislocations. The change in nonlinear ultrasonic testing results reflected the generation and evolution of dislocation structure during the low-cycle fatigue regime of the SLM 316L stainless steel specimen and revealed the early fatigue damage mechanism of this metal part. Compared with the classical FFT method, the EMD-ESI-FFT method is more sensitive in identifying the early damage in SLM 316L stainless parts induced by fatigue loading, which is equivalent to improving the early fatigue damage identification and diagnosis ability and can better ensure the service safety of important metal parts.