Despite the success of crack segmentation, the traditional segmentation strategy and networks are not necessarily suitable for fatigue cracks with unique visual features. Towards the indistinct crack features, a network named Fatigue Crack Unet (FC-Unet) was proposed, where the novel split attention mechanism was incorporated to boost diverse feature extraction. Scaled by various ratios, raw images were cropped and constituted three datasets to represent different segmentation strategies. FC-Unet was trained and tested on each dataset, where the class imbalance problem was alleviated by the adjustment of loss functions. Results showed that the segmentation performance is mainly limited to noise interference. Preserving abundant global contexts to distinguish noises, the global inference is the superior strategy to the previous local inference. Leveraging the wide receptive field in global inference, the down-sampling rate can be decreased to save resolution losses. Combining the focus-based and region-based loss functions, the accuracy of imbalanced data was further improved. Compared with nine classical networks, the proposed FC-Unet enjoyed a powerful backbone and achieved a superior metric of 83.1% mean intersection over union (MIoU).