Abstract: Abstract: A large amount of agricultural waste has been generated each year in China, particularly with about 900 million tons of crop straw and 260 million tons of tailings. The proper disposal can greatly contribute to the high utilization of agricultural waste in the environmental ecosystems, and the less surface pollution in farmland. However, the current resource utilization of agricultural waste has posed a great challenge, such as straw and livestock manure. It is a high demand to find a rational way for the sustainable production of agricultural waste. In this study, a drought-resistant and root-promoting substrate culture was fabricated to mix the compost and crop straw with clay, in order to improve the utilization rate of agricultural waste. A systematic investigation was made to clarify the effect of water-fertilizer coupling on the growth, yield, quality, water use efficiency (WUE), and partial factor productivity of fertilizer (PFP). Taking the tomatoes were grown on "Aegis 3041" as a test crop, nine water-fertilizer coupling treatments were set using substrate cultures, i.e., three groups of drip irrigation water W1, W2, and W3 (high water: 100% ET0, medium water: 80% ET0, low water: 60% ET0, where ET0 was the reference crop evapotranspiration), while three groups of fertilizer F1, F2 and F3 (N-P2O5-K2O) levels (high fertilizer: 240-115-137 kg/hm2, medium fertilizer: 180-88-121.2 kg/hm2, low fertilizer: 112-50-82 kg/hm2), and the CK was used as a control group with reference to the actual local production of water and fertilizer. A total of 10 coupled treatments were developed to comprehensively evaluate the tomato yield, WUE, PFP, and overall fruit quality. A genetic algorithm (GE) multi-objective optimization model was also established to optimize the evaluation. The results showed that the plant height of tomatoes in the substrate culture presented a trend of increasing and then decreasing, with the increase of irrigation amount during each fertility period. The mass, surface area, and length of root increased by 36.9%, 4.0%, and 6.3%, respectively, under the same fertilizer application conditions, compared with CK. Correspondingly, the substrate culture was effectively improved the plant height, stem thickness, root development, yield, quality, WUE, and PFP. The VIKOR method was used to comprehensively evaluate the fruit quality of each treatment. The fruit flavor quality and yield of tomatoes cultivated in substrate were significantly improved. The tomato flavor quality and yield were the best under the W3F1 treatment, and the benefit ratio was the smallest. The GE multi-objective optimization demonstrated that the best irrigation-fertilization treatment was W3F2 for the substrate culture, with the highest yield of 25.85 t/hm2, a lowest WUE of 13.77%, an optimum sugar to acid ratio of 9.51, and a benefit ratio of 0.357. Consequently, the substrate culture cultivation technology can be widely expected to save the water and fertilizer for the higher productivity and quality of fruits and vegetables, there by efficiently improving the utilization rate of agricultural waste resources. The effective way can be served to dispose of the agricultural non-point source pollution for the fewer carbon emissions in the sustainable crop production. The photovoltaic plus brick development can greatly contribute to transforming facility agriculture into natural agriculture in the future, such as the rich land resources in northwest China. This finding can also provide theoretical support to the efficient use of agricultural waste, as well as the rational management of water and fertilizer for the high-quality fruits and vegetables in modern agriculture.