The vibration signal of rolling bearing with variable operating conditions contains complex interference components, which will cause low fault diagnosis accuracy, especially in strong noise case. To solve this problem, we proposed a noise reduction method of rolling bearing with variable operating based on empirical wavelet transform and adaptive time-frequency peak filtering (EWT-ATFPF). Firstly, empirical wavelet transform (EWT) is used to obtain different frequency intrinsic mode functions (IMFs). Secondly, a modified adaptive window length formula for TFPF is constructed by combining the sampling ratio index and a fault sensitivity indicator that calculated by kurtosis and correlation coefficients of IMFs, which can better characterize the impact components. Thirdly, to balance noise reduction effect and the fidelity of IMFs, we proposed an improved time-frequency peak filtering (TFPF) method by adaptively adjusting its windows length. The adaptive method could be carried out using the proposed fault sensitivity indicator and window length formula, and the denoising IMFs could be obtained by ATFPF. Finally, the denoising vibration signal is reconstructed by using the denoising IMFs. The performance of fault diagnosis of the proposed method is verified by using simulated signal and bearing fault test data. The results show that the proposed EWT-ATFPF method could effectively achieve noise reduction under variable operating conditions.