This paper proposes a new signal noise level estimation approach by local regions. The estimated noise variance is applied as the threshold for an improved empirical mode decomposition(EMD) based signal denoising method. The proposed estimation method can effectively extract the candidate regions for the noise level estimation by measuring the correlation coefficient between noisy signal and a Gaussian filtered signal. For the improved EMD based method, the situation of decomposed intrinsic mode function(IMFs) which contains noise and signal simultaneously are taken into account. Experimental results from two simulated signals and an X-ray pulsar signal demonstrate that the proposed method can achieve better performance than the conventional EMD and wavelet transform(WT) based denoising methods. The proposed noise variance is applied as the threshold for an improved empirical mode decomposition (EMD) based signal denoising method. The proposed estimation method can effectively extract the candidate regions for the noise level estimation by measuring the correlation coefficient between noisy signal and a Gaussian filtered signal. For the improved EMD based method, the situation of decomposed intrinsic mode function (IMFs) which contains noise and signal are taken into account. Experimental results from two simulated signals and an X-ray pulsar signal demonstrate that the proposed method can achieve better performance than the conventional EMD and wavelet transform (WT) based denoising methods.