Soil microbial community is increasingly being used to assess ecosystem responses to disturbances and to provide an early indicator of ecosystem recovery. However, there is little field study to predict the patterns of microbial community during ecosystem restoration. In this study, to estimate the change on the soil bacterial diversity and community structure during native plant restoration after dioxin disaster that generated from the Vietnam War, we applied 16S metagenomics on un-affected forests and mimicking of three rehabilitated ages in central Vietnam based on dioxin concentrations and plant restoration status. Here, we found that dioxin contamination significant shaped soil bacterial community structure. Although the hypothesis that the bacterial community structures during restoration would gradually become more similar to those native state was highly supported by the shift in the bacterial community in the taxonomic and Bray-Curtis analysis, principal component analyses revealed a new trajectory deviating the native state with a cumulative percentage of 38.8 %. Besides, interestingly, reduction of species diversity was only detected in the intermediate and climax state instead of the pioneer state. Taken together, our results suggested dioxins significantly altered the soil bacterial community into a new pattern with diversity reduction and changing the trajectory of restoration.