The theories of empirical mode decomposition (EMD) and instantaneous frequency solution which are two parts of Hilbert-Huang Transformation (HHT) are discussed in the paper. We are focus on using the EMD to electrocardiogram (ECG) which can be decomposed into a limited number of intrinsic mode functions. Different thresholds are used to treat intrinsic mode function to achieve de-noising and then compared with the effect of wavelet transform de-noising. Hilbert-Huang Transform is demonstrated to be effective in removing the general noise of ECG.