In order to evaluate the effects of soils with different bacterial wilt disease incidences on nitrogen uptake efficiency of tomato plants, tomato was used as the test plant and soils with different disease incidences (12.5%, 21.9%, 40.0%, 59.4%, 83.3% and 91.6%) were collected to conduct a greenhouse pot experiment. The results showed that with the increase of initial soil bacterial wilt disease incidence, tomato plant biomass and nitrogen uptake efficiency showed a significant decreasing trend. There was no significant correlation between the contents of soil total N, ammonium N and nitrate N with plant N uptake efficiency at the beginning. No significant correlation between initial soil bacterial diversity and community composition with plant nitrogen absorption efficiency; however, significant correlation was observed between bacterial community change based on OTU analysis and plant N uptake efficiency. The relative abundances of Lysobacter and Luteimonas showed a significant and positive correlation with plant N uptake efficiency, and among which Lysobacter also showed a significant and negative correlation with tomato bacterial wilt disease incidence. In conclusion, this study observed that the initial bacterial community in soil with continuous cropping obstacle, but not nitrogen nutritional status, was correlated with the plant nitrogen uptake.