An accurate iris segmentation method is crucial for the iris recognition system. The conventional iris segmentation algorithms have poor adaptability when applied to heterogeneous iris databases. Therefore, researchers have applied deep learning to the field of iris segmentation. A modified U-Net is proposed to perform the iris segmentation for heterogeneous iris databases, referred to as DropBlock and modified shortcut branch U-Net. The main work is as follows: first, EfficientNetV2 based on DropBlock is used as convolutional blocks of U-Net to improve the ability of feature extraction and generalization of the network. Second, an improved shortcut branch structure is proposed for U-Net to reduce the loss of information during the downsampling process. The experimental results on the CASIA-iris-interval-v4, IITD, and UBIRIS.v2 iris databases demonstrate that this method can not only have good versatility but also provide higher accuracy on heterogeneous databases. Compared with some state-of-the-art fusion methods, the proposed method has a significant performance advantage.