Purpose <p>Humus, as a vital component of the soil stable carbon pool, is critical for the enhancement of the carbon sink function of wetlands. However, little research has focused on the influencing factors and microbial mechanisms underlying the humification process in estuarine wetland soils. Here the spatial distribution pattern of soil humification intensity, its influencing factors, and associated microbial mechanisms are clarified in this study.</p> Materials and methods <p>The Jiuduansha wetland in the Yangtze River estuary was utilized as a representative case to elucidate the spatial distribution patterns of humification and mineralization intensity by measuring the ratio of humus to soil organic carbon (SOC) and soil respiration (SR). Furthermore, by examining the physical and chemical properties of plant and soil as well as the structure of soil microbial communities, combined with statistical analysis, the factors and mechanisms affecting the humification process of estuarine wetlands are investigated.</p> Results and discussion <p>Our results show that, the humification intensity was higher in low tidal flats than in high tidal flats, and greater in coastal areas compared to riparian areas, while mineralization intensity exhibited an opposite pattern in the Jiuduansha wetland. Some specific microorganisms such as <i>Syntrophorhabdus</i>, <i>Tolumona</i>s and <i>Cystofilobasidium</i> played a crucial role in regulation of the humification and mineralization processes, whereas dominant microorganisms had a less significant impact. The results of PCA showed that soil moisture and salinity were the two factors with the highest percentage of weights affecting the variation of specific microbial communities associated with the soil mineralization and humification processes, while the plant lignin input was not significantly correlated with specific microbial communities.</p> Conclusions <p>Soil moisture and salinity are vital causes of spatial variation in specific microorganisms associated with mineralization and humification process, while plant-induced dominant microorganisms exert minimal influence on the spatial differences of soil humification intensity. This study provides theoretical guidance for the enhancement of carbon sequestration in estuarine wetlands while mitigating the effects of climate change, as well as preserving the important ecological functions of their natural landscapes.</p>