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Moderate spatial resolution (MSR) satellite images, which hold a trade-off among radiometric, spectral, spatial and temporal characteristics, are extremely popular data for acquiring land cover information. However, the low accuracy of existing classification methods for MSR images is still a fundamental issue restricting their capability in urban land cover mapping. In this study, we proposed a hybrid convolutional neural network (H-ConvNet) for improving urban land cover mapping with MSR Sentinel-2 images. The H-ConvNet was structured with two streams: one lightweight 1D ConvNet for deep spectral feature extraction and one lightweight 2D ConvNet for deep context feature extraction. To obtain a well-trained 2D ConvNet, a training sample expansion strategy was introduced to assist context feature learning. The H-ConvNet was tested in six highly heterogeneous urban regions around the world, and it was compared with support vector machine (SVM), object-based image analysis (OBIA), Markov random field model (MRF) and a newly proposed patch-based ConvNet system. The results showed that the H-ConvNet performed best. We hope that the proposed H-ConvNet would benefit for the land cover mapping with MSR images in highly heterogeneous urban regions.