Using studied ECG sampling system, the analog signals of electrocardiograph is magnified and filtered,sending into the sampling card in computer, the sampling frequence is 1 000 Hz, the 5 minutes sampling signal is saved to hard disk. Using modern spectrum analysis method and FFT, the specific value VLF/HF of Heart Rate Variability (HRV)of 19 healthy individuals and 10 hyperthyroid is analysed .It is found that the significant difference of the specific value VLF/HF between the healthy individuals and hyperthyroid.There are no especial advantage and distinctness by using the modern spectrum analysis method or FFT to study balance the specific value VLF/HF between the healthy individuals and hyperthyroid. The result shows that the spectrum analysis method is relly an effective measure to analyze independence nerve abnormalities of hyperthyroid.