Excessive agricultural investment brought about by increased multiple-cropping index may compromise environmental sustainability. There are few studies on the sustainability of diversified multi-cropping systems in the Yangtze River Basin (YRB). Therefore, this study selected five representative locations in the YRB. According to the local climate characteristics and food demand, diversified multi-cropping systems were designed, and the main local winter crops were selected as the previous crops of the corn–soybean strip compound cropping system, with the local traditional double-cropping model as the control (CK). The emergy evaluation method was introduced to quantitatively compare the efficiency and sustainability of diversified multi-cropping systems in the YRB. The results showed that by incorporating soybean by intercropping with corn, compared with the CK, the total energy input, annual energy output, and annual economic output increased by 15.80%, 9.78%, and 33.12% on average, respectively. The unit emergy value (UEV) and unit non-renewable value (UNV) increased by 6.03% and 5.98%, respectively; the emergy yield ratio (EYR) and environmental loading ratio (ELR) decreased by 0.91% and 0.44%, respectively; the emergy sustainability index (ESI) was the same. In the third mature crop selection, compared with that of corn, the ELR of soybean decreased by 14.32%, and the ESI increased by 18.55%. In addition, the choice of winter crops plays a vital role in the system’s efficiency and sustainability. Compared with those of other winter crops, the annual economic outputs of potato (upper reaches of the YRB), potato or forage rape (middle reaches of the YRB), and wheat (lower reaches of the YRB) increased by 51.02%, 32.27%, and 0.94%, respectively; their ESI increased by 71.21%, 47.72%, and 12.07%, respectively. Potato–corn/soybean or potato/corn/soybean (upper reaches of the YRB), forage rape–corn/soybean or potato/corn/soybean (middle reaches of the YRB), and wheat–corn/soybean (lower reaches of the YRB) were chosen to facilitate the coexistence of high economic benefits and environmental sustainability. Additionally, promoting mechanization and reducing labor input were essential to improve the efficiency and sustainability of multi-cropping systems. This study would provide a scientific basis and theoretical support for the development of efficient and sustainable multiple-cropping systems in the dryland of the YRB.
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