Excessive application of chemical fertilizer and continuous cropping in plastic greenhouse resulted in soil quality decline. The decrease of soil C/N ratio and the imbalance of soil carbon pool structure have brought new challenges to soil health, crop yield and sustainable agricultural development. Objectives The experiment was set up to explore the effect of modified biochar on soil bacterial community structure, and the correlation between soil environmental factors and bacterial community structure changes. Based on the plot experiment in the field, the effect of modified biochar was studied via high-throughput MiSeq sequencing. Results Compared with the control (CK), the modified biochar (T) significantly increased soil water content, microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) content and the ratio of MBC and MBN by 7.92%, 24.58%, 2.07% and 18.95%. Diversity index analysis showed that the application of modified biochar significantly increased the Shannon index, ACE index and Chao1 index of the bacterial community by 3.05%, 5.07% and 5.24%. Compared with the control, the modified biochar decreased the relative abundance of Actinobacteriota and Chloroflex by 6.81% and 2.19%, and increased the relative abundance of Proteobacteria and Acidobacteriota by 7.34% and 12.52%. Correlation analysis shows that soil bulk density and water content may be important related factors that affect bacterial community structure. Conclusions This study provides a theoretical basis for the directional control of modified biochar in the soil microecological environment in plastic greenhouse, which is conducive to healthy and sustainable farming.