Mangrove soils host diverse microbial taxa. However, our knowledge of how these microbial taxa respond to bridge construction remains limited. In this study, the changes of major microbial taxa (including archaea, bacteria, and fungi) under two different bridge construction methods (Sheet pile cofferdam, SP; Steel casing pipe, SC)) and adjacent undisturbed mangrove forests (UD) were investigated. The results showed that the alpha diversities of bacteria and archaea were significantly lower under SC and SP than under UD. In contrast, the alpha diversity of fungi showed no significant difference between the three habitats, implying that prokaryotic microbiota of the mangrove soil is more sensitive to bridge construction disturbance compared to the fungal community. Similarly, bridge construction decreased beta diversities of bacteria and archaea, while increasing 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. In conclusion, mangrove soil prokaryotic communities are more sensitive to bridge construction than fungal communities. Therefore, future engineering projects should prioritize monitoring changes in prokaryotic diversity.