Improving the quality of breast ultrasound images is of great significance for clinical diagnosis which can greatly boost the diagnostic accuracy of ultrasonography. However, due to the influence of ultrasound imaging principles and acquisition equipment, the collected ultrasound images naturally contain a large amount of speckle noise, which leads to a decrease in image quality and affects clinical diagnosis. To overcome this problem, we propose an improved denoising algorithm combining multi-filter DFrFT (Discrete Fractional Fourier Transform) and the adaptive fast BM3D (Block Matching and 3D collaborative filtering) method. Firstly, we provide the multi-filtering DFrFT method for preprocessing the original breast ultrasound image so as to remove some speckle noise early in fractional transformation domain. Based on the fractional frequency spectrum characteristics of breast ultrasound images, three types of filters are designed correspondingly in low, medium, and high frequency domains. And by integrating filtered images, the enhanced images are obtained which not only remove some speckle noise in background but also preserve the details of breast lesions. Secondly, for further enhancing the image quality on the basis of multi-filter DFrFT, we propose the adaptive fast BM3D method by introducing the DBSCAN-based super pixel segmentation to block matching process, which utilizes super pixel segmentation labels to provide a reference on how similar it is between target block and retrieval blocks. It reduces the number of blocks to be retrieved and make the matched blocks with more similar features. At last, the local noise parameter estimation is also adopted in the hard threshold filtering process of traditional BM3D algorithm to achieve local adaptive filtering and further improving the denoising effect. The synthetic data and real breast ultrasound data examples show that this combined method can improve the speckle suppression level and keep the fidelity of structure effectively without increasing time cost.