Globally, sea levels are rising due to climate change which would influence the salinity levels in mangroves. In the framework of this study, we focused on the influence of salinity and differences of forest structure on the fine root biomass (FRB) and carbon stocks in the Sundarbans mangrove forest, Bangladesh. Also, the relationships FRB to different stand structural parameters were investigated using the data obtained from 50 sample plots (100 sq. m each) in different salinity zones in Sundarbans. Four random soil samples (30 cm in length) were taken within study plots, which were further divided into 10 cm, 20 cm, and 30 cm to identify the most active soil layer for FRB stocks. Results suggest differences in forest structural parameters and diversity indices with salinity changes in different saline zones. The low and medium saline zone is dominated by Heriteira fomes, while Excoecaria agallocha dominates the high saline zone. The carbon stocks (Mg C ha−1) in Sundarbans show a significant decrease with increasing salinity in different saline zones, e.g. oligohaline (252 ± 60.2), mesohaline (199 ± 37.7), and polyhaline (171 ± 20.0) zone. FRB carbon (Mg C ha−1) allocation in different saline zones also followed a decreasing order, such as oligohaline (12.8), mesohaline (7.9), and polyhaline (7.3). Fine root biomass showed a decreasing trend with increasing soil depth, where the differences, however, were not significant (p > 0.05) among the soil layers. Our results provide evidence on FRB variations in Sundarbans, which has implications on the mangrove species conservation and management. The mature stands at different saline zones of Sundarbans mangrove forest, Bangladesh has a high fine root biomass, which is valuable for mangrove restoration and the studied species plantation in the shore line or coastal area which can help to decrease the erosion effects of tidal inundation.