The performance of semantic segmentation in remote sensing, based on deep learning models, depends on the training data. A commonly encountered issue is the imbalanced long-tailed distribution of data, where the head classes contain the majority of samples while the tail classes have fewer samples. When training with long-tailed data, the head classes dominate the training process, resulting in poorer performance in the tail classes. To address this issue, various strategies have been proposed, such as resampling, reweighting, and transfer learning. However, common resampling methods suffer from overfitting to the tail classes while underfitting the head classes, and reweighting methods are limited in the extreme imbalanced case. Additionally, transfer learning tends to transfer patterns learned from the head classes to the tail classes without rigorously validating its generalizability. These methods often lack additional information to assist in the recognition of tail class objects, thus limiting performance improvements and constraining generalization ability. To tackle the abovementioned issues, a graph neural network based on the graph kernel principle is proposed for the first time. By leveraging the graph kernel, structural information for tail class objects is obtained, serving as additional contextual information beyond basic visual features. This method partially compensates for the imbalance between tail and head class object information without compromising the recognition accuracy of head classes objects. The experimental results demonstrate that this study effectively addresses the poor recognition performance of small and rare targets, partially alleviates the issue of spectral confusion, and enhances the model’s generalization ability.