Few-shot class-incremental learning was introduced to solve the model adaptation problem for new incremental classes with only a few examples while still remaining effective for old data. Although recent state-of-the-art methods make some progress in improving system robustness on common datasets, they fail to work on fine-grained datasets where inter-class differences are small. The problem is mainly caused by: (1) the overlapping of new data and old data in the feature space during incremental learning, which means old samples can be falsely classified as newly introduced classes and induce catastrophic forgetting phenomena; (2) lacking discriminative feature learning ability to identify fine-grained objects. In this paper, a novel Pseudo-set Frequency Refinement (PFR) architecture is proposed to tackle these problems. We design a pseudo-set training strategy to mimic the incremental learning scenarios so that the model can better adapt to novel data in future incremental sessions. Furthermore, separate adaptation tasks are developed by utilizing frequency-based information to refine the original features and address the above challenging problems. More specifically, the high and low-frequency components of the images are employed to enrich the discriminative feature analysis ability and incremental learning ability of the model respectively. The refined features are used to perform inter-class and inter-set analyses. Extensive experiments show that the proposed method consistently outperforms the state-of-the-art methods on four fine-grained datasets.