An environmentally sustainable cultivated grassland at the edge of the Junggar Desert Basin in China is vital for the ecological conservation of the mountain-basin system (MBS) in the arid region of Central Asia and the stable settlement of herdsmen in the northern China. To evaluate the sustainability of sown systems, this study applied emergy and economic analysis to three traditional sown systems, silage corn (SC), oil sunflower (OS), and seed melon (SM), and three innovative sown systems, leafy king monocropped (LM), leafy king-sudangrass intercropped (LSI) and algonquin-sudangrass intercropped (ASI), in a cultivated grassland at the edge of the Junggar Desert Basin. The emergy results revealed that all systems required 85.65%–90.32% of emergy investments from outside systems, and 74.17%–84.46% of the investments were nonrenewable emergy inputs. The emergy sustainability ratio revealed that ASI, LSI and LM had superior ecological benefits with lower environmental burdens than SC, OS and SM. The economic analysis illustrated that OS and ASI had high economic profits, while ASI, LSI and LM had high income-to-cost ratios. LSI and ASI could achieve both ecological and economic benefits. The chemical fertilizer and irrigation water simulations indicated that the sustainability of all these systems could be enhanced by applying drip irrigation and reducing chemical fertilizer by 20%. Therefore, water-saving irrigation and renewable resource utilization need to be implemented. Appropriate adjustments to the plantation structure and long-term financial and policy support for cultivated grassland construction are recommended. Advanced cultivated technology should be investigated and promoted. Additionally, the rationally allocated and scientifically managed cultivated grassland at the edge of desert basin can be an optimized strategy for sustainable development of ecological and economic in similar MBSs of the arid regions of Central Asia.