A Cross-correlation Integral based Unintentional Modulation Identification (CCI-UMI) method is proposed for Power Amplifier (PA) fingerprinting, assuming that the PA is excited by continuous signals of the same frequency. The model of the PA and the theory probability density along trajectory is presented. Then an algorithm is given, using multi-scale comparison to distinguish the two signals with tiny difference. The actual measurement experiment of the signal generator shows that the developed CCI-UMI method is better than the Power Spectral Density based method and the Phase Space Difference method in lower SNR.