Deep models have been shown to tend to fit the target function from low to high frequencies (a phenomenon called the frequency principle of deep learning). One may hypothesize that such property can be leveraged for better training of deep learning models, in particular for segmentation tasks where annotated datasets are often small. In this paper, we exploit this property to propose a new training method based on frequency-domain disentanglement. It consists of three main stages. First, it disentangles the image into high- and low-frequency components. Then, the segmentation network model learns them separately (the approach is general and can use any segmentation network as backbone). Finally, feature fusion is performed to complete the downstream task. The method was applied to the segmentation of the red and dentate nuclei in Quantitative Susceptibility Mapping (QSM) data and to three tasks of the Medical Segmentation Decathlon (MSD) challenge under different training sample sizes. For segmenting the red and dentate nuclei and the heart, the proposed approach resulted in considerable improvements over the baseline (respectively between 8 and 16 points of Dice and between 5 and 8 points). On the other hand, there was no improvement for the spleen and the hippocampus. We believe that these intriguing results, which echo theoretical work on the frequency principle of deep learning, are of interest for discussion at the conference. The source code is publicly available at: https://github.com/GuanghuiFU/frequency_disentangled_learning