Cluster analysis of apple juice is an important method in the quality identification of fruit juice. However, the traditional principal component analysis (PCA) is to reduce the dimension of high dimensional data and to achieve clustering by way of score value. Experiments have found that this clustering method is not suitable for real samples with fluorescence overlap. In this paper, we propose a processing mechanism to optimize the derivative of the fluorescence spectrum. When the derivative is calculated, we can amplify the spectral difference of the similar matter and improve the ability of the PCA to achieve the best effect of clustering. Experiments show that the optimized method for the actual sample classification accuracy rate of 100%, which can fully realize the type of commercially available apple juice beverage distinction and achieve the practical application of quality testing.