In recent years, it has been difficult for multilabel classification to obtain complete multilabel data in real-world applications, and even a large number of labels for training samples are randomly missed. As a result, the classification task of incomplete multilabel data with missing labels faces formidable challenges. This paper presents a two-stage-neighborhood-based multilabel classification method for incomplete data with missing labels in neighborhood decision systems. First, to solve the problem of selecting the neighborhood radius manually, as well as balancing the samples in the neighborhood, the neighborhood radius based on the feature distribution function is defined, and the differences and similarities between samples through the identifiable and indiscernible matrices are, respectively, computed. Then, a restoration method for missing feature values is proposed for use in the first stage. Second, to consider the nonlinear relationship among features, a neighborhood-based fuzzy similarity relationship between samples is investigated based on the Gaussian kernel function. By integrating the fuzzy similarity relationship matrix, label-specific feature matrix, and label correlation matrix, an objective function based on the regression model is presented, the optimal solutions to the label-specific feature and label correlation matrices based on the gradient descent strategy are provided, and a new multilabel classification method with missing labels is developed during the second stage. Finally, two-stage multilabel classification algorithms are designed. Experiments on 18 multilabel data sets demonstrate that our designed algorithms are effective not only for recovering missing feature values, but also for improving the classification performance of data with missing labels.