The objective of this study is intended to explore the effect of maintain high efficiency water and fertilizer supply for improving the tomato production and soil bacterial communities by negative pressure irrigation (NPI) in greenhouse. The pot culture experiments consisted of three irrigation treatments: conventional irrigation (CI), drip irrigation (DI) and NPI, which have been conducted in greenhouse for two consecutive years. The study found that NPI reduced water consumption remained stable with slight variations on dynamic soil water content, as well as increased the water use efficiencies compared with CI and DI, respectively. The NPI reduced water consumption by 20% and 18% compared to CI in 2016 and 2017, respectively. Under NPI treatment, the variations in soil water content were stabilized, within the range of 12.3-14.7% in the two years, which was smaller than that of CI and DI treatments of 8.6-15.6%. Moreover, the tomato yields, fruit quality, uptake quantitates of nutrition and soil rhizosphere microbial diversity were increased in the NPI treatment comparison with the CI and DI treatments. With NPI, the yield of tomato was significantly increased by 26% and 8, 41 and 17% compared to that under CI and DI treatments in 2016 and 2017, respectively. NPI was also considered to benefit plant growth by increasing the abundances of Bacillus, Streptomyces and Pseudolabrys at the genus level. Therefore, NPI should be utilized as an advanced technique for saving water and producing high yields in future sustainable agriculture.