As a traditional agricultural production base in China, the Middle Yangtze Plain (MYP) is a typical region to explore the intensification, large-scale, and agglomeration of agricultural land, and its crop planting situation is sensitive to changes in national agricultural policy and economic development. So far, the research of crop remote sensing extraction mainly has focused on the areas with simple crops rotation patterns, by using short-time sequence remote sensing data with low spatial resolution. The objective of this study was to address how to accurately map the spatial distribution of main crops considering their spectral and phenological features, and what characteristics of spatio-temporal patterns dynamics of crops occurred in the MYP in 1990–2020. Based on Landsat and MODIS data, using the Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM) as well as the raster-based spectral and phenological differential change method (RSPDCM), this study mapped the spatial distribution of main crops (rice, cotton, maize, soybean, rapeseed and winter wheat) in the MYP during 1990–2020 and analyzed their planting characteristics. The RSPDCM has a good overall accuracy of more than 89%. The planting characteristics of the main crops were highly intensive and agglomerate double-cropping rotation in the MYP’s paddy field. Rice and rapeseed were the two most important crops, accounting for 74.75% of the annual planting area. The highly intensive and large-scale areas were mainly distributed in the Dongting Lake Plain (DTLP) and Poyang Lake Plain (PYLP), while the highly agglomerate areas of main crops were mainly distributed in the Jianghan Plain (JHP). This study innovatively provides a high-precision multi-cropping spatial dynamic mapping method and basic information, which is helpful to realize high-precision remote sensing extraction of crops in different regions of the world and provide basic data for optimizing the allocation of agricultural production resources in top grain-producing areas.