Clustering algorithms have the characteristics of being simple and efficient and can complete calculations without a large number of datasets, making them suitable for application in noise reduction processing for audio module mass production testing. In order to solve the problems of the NMF algorithm easily getting stuck in local optimal solutions and difficult feature signal extraction, an improved NMF audio denoising algorithm combined with K-means initialization was designed. Firstly, the Euclidean distance formula of K-means has been improved to extract audio signal features from multiple dimensions. Combined with the initialization strategy of K-means decomposition, the initialization dictionary matrix of the NMF algorithm has been optimized to avoid getting stuck in local optimal solutions and effectively improve the robustness of the algorithm. Secondly, in the sparse coding part of the NMF algorithm, feature extraction expressions are added to solve the problem of noise residue and partial spectral signal loss in audio signals during the operation process. At the same time, the size of the coefficient matrix is limited to reduce operation time and improve the accuracy of feature extraction in high-precision audio signals. Then, comparative experiments were conducted using the NOIZEUS and NOISEX-92 datasets, as well as random noise audio signals. This algorithm improved the signal-to-noise ratio by 10–20 dB and reduced harmonic distortion by approximately −10 dB. Finally, a high-precision audio acquisition unit based on FPGA was designed, and practical applications have shown that it can effectively improve the signal-to-noise ratio of audio signals and reduce harmonic distortion.