The maintenance of vegetable yield, the improvement of vegetable quality, and the utilization of vegetable residue are the top priorities for developing sustainable facility agriculture. To explore the residue resource utilization and the high quality and yield of tomatoes in solar greenhouses, conventional fertilization was used as the control (CK) in this study. To explore the effects of cultivation with tomato residues and B. subtilis (BS) five treatments were carried out as follows: 1. tomato residues (TC); 2. B. subtilis (BS); 3. tomato residues + B. subtilis (TC-BS); 4. double tomato residues (2TC) and 5. double tomato residues + B. subtilis (2TC-BS). The tomato growth, physiology, yield, quality, soil physicochemical traits, nutrient content, enzyme activity, and bacterial diversity were measured. The results showed that compared with CK, the synergy of TC and BS was important in improving tomato yield and soil quality. TC-BS and 2TC-BS significantly increased the plant height, root activity, total chlorophyll content, and net photosynthetic rate with up to 10.98% and 10.95% increases in yield, respectively. The tomato fruit quality such as the lycopene, soluble sugar, soluble protein, and vitamin C (VC) contents were also significantly increased. Additionally, 16S rDNA sequencing results indicated that the TC-BS and 2TC-BS significantly increased the diversity of soil bacteria. In conclusion, increasing the application of B. subtilis along with incorporating tomato residues can significantly improve the soil environment, enrich the beneficial microorganisms, and promote tomato growth, its yield, and quality.