The spatial pattern and temporal variation in paddy rice areas captured by remote sensing imagery provide an effective way of performing crop management and developing suitable agricultural policies. However, fragmented and scattered rice paddies due to undulating and varied topography, and the availability and quality of remote sensing images (e.g., frequent cloud coverage) pose significant challenges to accurate long-term rice mapping, especially for traditional pixel and phenological methods in subtropical monsoon regions. This study proposed a superpixel and deep-learning-based time series method to analyze Landsat time series data for paddy rice classification in complex landscape regions. First, a superpixel segmentation map was generated using a dynamic-time-warping-based simple non-iterative clustering algorithm with preprocessed spectral indices (SIs) time series data. Second, the SI images were overlaid onto the superpixel map to construct mean SIs time series for each superpixel. Third, a multivariate long short-term memory full convolution neural network (MLSTM-FCN) classifier was employed to learn time series features of rice paddies to produce accurate paddy rice maps. The method was evaluated using Landsat imagery from 2000 to 2020 in Cengong County, Guizhou Province, China. Results indicate that the superpixel MLSTM-FCN achieved a high performance with an overall accuracy varying from 0.9547 to 0.9721, which presents an 0.17–1.23% improvement compared to the random forest method. This study showed that combining spectral, spatial, and temporal features with deep learning methods can generate accurate paddy rice maps in complex landscape regions.