Clustering analysis, a key step for many data mining problems, can be applied to various fields. However, no matter what kind of clustering method, noise points have always been an important factor affecting the clustering effect. In addition, in spectral clustering, the construction of affinity matrix affects the formation of new samples, which in turn affects the final clustering results. Therefore, this study proposes a noise cutting and natural neighbors spectral clustering method based on coupling P system (NCNNSC-CP) to solve the above problems. The whole algorithm process is carried out in the coupled P system. We propose a natural neighbors searching method without parameters, which can quickly determine the natural neighbors and natural characteristic value of data points. Then, based on it, the critical density and reverse density are obtained, and noise identification and cutting are performed. The affinity matrix constructed using core natural neighbors greatly improve the similarity between data points. Experimental results on nine synthetic data sets and six UCI datasets demonstrate that the proposed algorithm is better than other comparison algorithms.