In the measurement of electronic speckle pattern interferometry, interference fringes contain much noise that affects the subsequent phase extraction. To solve the problem that the bilateral filtering cannot effectively remove high noise, a joint bilateral filtering combined with the windowed Fourier filtering is proposed to deal with electronic speckle pattern interferometry fringes with high noise. In the method, an image after initial processing by the windowed Fourier filtering is introduced as the guiding map of the joint bilateral filtering. Then, an improved similarity factor of pixel value is introduced to provide more reliable guiding information and better filtering effect. The proposed method is applied to four different simulated electronic speckle pattern interferometry fringes with high, medium, low and variable densities and the real electronic speckle pattern interferometry fringes with high noise. In addition, the proposed method is compared with the bilateral filtering and the windowed Fourier filtering. Experimental results show that the fringe obtained by joint bilateral filtering is smoothest, and the structure is the most complete. The peak signal to noise ratio of the simulated fringe filtered by the new method is improved by 1. 0 ~ 4. 2 dB, the structural similarity index and edge preservation index are the highest, and the mean square error of the phase is the smallest. In addition, the proposed method is more convenient to adjust, and the calculation time for a 330×330 simulated fringe is only about 4 s.