Abstract Aiming at addressing the issues of colour deviation and clarity reduction in digital pathological imaging systems caused by complex environmental interferences such as uneven slice thickness, sample jitter, and background noise, this paper proposes a multi-saliency-guided filtering fusion enhancement method that combines energy saliency and Gaussian saliency. Firstly, a series of Gamma correction and spatial linear saturation adjustments are applied to enhance the contrast and colour saturation of blurred images, resulting in a sequence of pseudo-exposure images with improved contrast and saturation. Then, the pseudo-exposure images are decomposed into base and detail layers, and the fusion rules of energy saliency and Gaussian saliency-guided filtering are applied to each layer separately. Finally, clear microscopic images are obtained through two-scale reconstruction. This method overcomes the limitations of conventional deblurring algorithms that rely on prior estimation of scene depth and complex depth mapping processes. Experimental results on a dataset of cytological bright-field microscopic imaging samples show that the clarity evaluation metrics, including peak signal-to-noise ratio, root mean square error, and structural similarity index, have significantly improved, indicating that the proposed method can effectively improve the colour fidelity of the samples while eliminating noise interference and enhancing the clarity of cellular texture structures.