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The segmentation and classification of leaves in plant images are a great challenge, especially when several leaves are overlapping in images with a complicated background. In this paper, the segmentation and classification of leaf images with a complicated background using deep learning are studied. First, more than 2500 leaf images with a complicated background are collected and artificially labeled with target pixels and background pixels. Two-thousand of them are fed into a Mask Region-based Convolutional Neural Network (Mask R-CNN) to train a model for leaf segmentation. Then, a training set that contains more than 1500 training images of 15 species is fed into a very deep convolutional network with 16 layers (VGG16) to train a model for leaf classification. The best hyperparameters for these methods are found by comparing a variety of parameter combinations. The results show that the average Misclassification Error (<inline-formula><math display="inline"><semantics><mrow><mi>M</mi><mi>E</mi></mrow></semantics></math></inline-formula>) of 80 test images using Mask R-CNN is 1.15%. The average accuracy value for the leaf classification of 150 test images using VGG16 is up to 91.5%. This indicates that these methods can be used to segment and classify the leaf image with a complicated background effectively. It could provide a reference for the phenotype analysis and automatic classification of plants.