Mangrove soils host diverse microbial taxa, however, our knowledge of how these microbial taxa respond to bridge construction remains limited. In this study, we investigated the changes of major microbial taxa (including archaea, bacteria, and fungi) under two different bridge construction methods (Sheet Pile Cofferdam (SP) and Steel Casing Pipe (SC)) and adjacent undisturbed mangrove forests (Undisturbed mangrove, UD). Our results showed that the alpha diversity of bacteria and archaea was significantly lower in the SC and SP habitats than in the UD habitat. In contrast, the alpha diversity of the fungal showed no significant difference between the three habitats, implying that the prokaryotic microbiota of the mangrove soil is more sensitive to bridge construction disturbance compared to the fungal community. Similarly, bridge construction decreased the beta diversity of bacteria and archaea, while increasing the beta diversity of fungi. Species replacement, rather than changes in species richness, mainly contributed to the changes in the composition of the microbial community. Additionally, microbial communities residing in bridge construction habitats exhibited lower community dissimilarity than UD, and fungal communities were more stable than bacteria and archaea. Soil pH and C/N ratio are the most important environmental factors in shaping soil microbial communities. Overall, our study revealed different responses of soil’s multiple microbial groups in mangrove ecosystems to bridge construction disturbance. This study has important implications for understanding and conserving biodiversity in natural ecosystems under the influence of human activities.