Root morphology and its components’ behavior could show a considerable response under multiple water application points per plant to help the ultimate effect of fruit yield and fruit quality. In this study, a comparison of a single emitter per plant was made with two, three, and four emitters per plant under drip irrigation and two irrigation levels (full irrigation 100% and deficit irrigation 75% of crop evapotranspiration) to investigate their effects on physiological parameters, root, yield, and their associated components for potted cherry tomato under greenhouse conditions in Jiangsu-China. The experimental results showed that the plants cultivated in the spring-summer planting season showed significantly higher results than the fall-winter planting season due to low temperatures in the fall-winter planting season. However, the response root length, root average diameter, root dry mass, leaf area index, photosynthetic rate, transpiration rate, fruit unit fresh weight, the number of fruits, and pH were increased by multiple emitters per plant over a single emitter per plant, but total soluble solids decreased. Besides, a decreasing trend was observed by deficit irrigation for both planting seasons, and vice versa for the case for tomato total soluble solids. Due to an increase in measured parameters for multiple emitters per plant over a single emitter per plant, the yield, water use efficiency, and water use efficiency biomass significantly increased by 18.1%, 17.6%, and 15.1%, respectively. The deficit irrigation caused a decrease in the yield of 5% and an increase in water use efficiency and water use efficiency biomass of 21.4% and 22.9%, respectively. Two, three, and four emitters per plant had no significant effects, and the obtained results were similar. Considering the root morphology, yield, water use efficiency, water use efficiency biomass, and fruit geometry and quality, two emitters per plant with deficit irrigation are recommended for potted cherry tomato under greenhouse conditions. The explanation for the increased biomass production of the plant, yield, and water use efficiency is that two emitters per plant (increased emitter density) reduced drought stress to the roots, causing increased root morphology and leaf area index and finally promoting the plant’s photosynthetic activity.