Optimizing cultivation methods is crucial for enhancing the productivity and sustainability of protected agriculture in water-limited regions. This study systematically evaluated the effects of three cultivation methods—bucket, non-woven bag, and underground trough cultivation—on the root-zone environment, growth, yield, and quality of greenhouse-grown tomatoes (Solanum lycopersicum L. ‘Provence’) in a Gobi Desert facility. Key root-zone parameters (substrate temperature, moisture, and electrical conductivity) and plant agronomic traits (plant height, stem diameter, leaf number, and SPAD) were monitored throughout the growth cycle. Final yield and fruit quality indicators (lycopene, soluble sugars, and vitamin C) were analyzed. The results demonstrated that bucket and underground trough cultivation created a more stable root-zone environment, with better moisture retention and temperature regulation than bag cultivation. These methods significantly improved plant growth, with yield per plant increasing by 23.18% and 18.18% under bucket and underground trough cultivation, respectively, alongside enhanced fruit quality metrics. In conclusion, bucket and underground trough cultivation effectively optimize the root-zone environment, leading to superior tomato growth, yield, and quality compared to traditional non-woven bag cultivation. These methods show significant potential for application in arid and semi-arid regions to support sustainable and efficient greenhouse production.