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Tropical forests are well-known as highly productive terrestrial ecosystems, which contribute significantly to the global carbon (C) cycle. Studies indicate a correlation between the structural diversity of forests and carbon stocks in the overall forest carbon stocks, and this relationship varies across tropical ecosystems. Understanding this connection is crucial to preventing the transfer of threats to unprotected areas when safeguarding specific forests. The present study was conducted in the undisturbed natural forests of Rema Kalenga Wildlife Sanctuary, Habigonj, Bangladesh. The study aimed to estimate C stocks within the soil-vegetation system of this forest ecosystem and elucidate relationships with stand structural diversity, focusing on vertical stratification and spatial association of tree species. Stand-level C stock models, constructed through tree-level carbon stocks using allometric equations, were based on stand variables such as basal area and mean or dominant tree height. Results identified five canopy strata, with strata two and three accounting for 60% of C stocks. The importance value index of tree species demonstrated a significant association with the C stocks contribution of tree species. The total ecosystem carbon stock ranged from 185 to 220 Mg ha−1, with aboveground 103 to 132 Mg ha−1, belowground 21 to 26 Mg ha−1, litter 2.4 to 4.4 Mg ha−1, dead wood 0.5 to 4.9 Mg ha−1 and soil 11 to 44 Mg ha−1. Species diversity indices exhibited weaker relationships with C stocks, while Pielou's evenness index demonstrated a strong negative relationship (P < 0.05) to C stocks. This comprehensive assessment provides insights into the C dynamics of the forest ecosystem. It offers valuable information for policymakers devising climate change mitigation strategies through the conservation management of tropical forests as crucial C sinks.