Purpose <p>Coastal saline soils are characterized by high salt ion concentrations, high pH values and low organic matter contents. Ectomycorrhizal (ECM) fungi can promote plant growth and increase soil carbon inputs. However, it is not clear how ECM plants impact soil organic carbon (SOC) in coastal saline soils.</p> Materials and methods <p>Coastal saline soils were collected <i>in situ</i>, and ECM <i>P. thunbergii</i> seedlings with two <i>Suillus</i> species were separately planted in the soils. Changes in SOC, dissolved organic carbon (DOC) and microbial biomass carbon (MBC) were determined. The specific changes in soil DOC were also clarified via three-dimensional fluorescence spectrometry, and the changes in soil microbial communities were clarified via high-throughput sequencing.</p> Results and discussion <p>After one year, the SOC increased by 43.1% and 50.6%, respectively. The proportion of soil macroaggregates was higher in coastal saline soils, and the organic carbon contents of difficult-to-decompose silt and clay aggregates were higher by 3.2 and 3.3 times, respectively. The content of DOC increased with the conversion to tryptophan protein substances and soluble microbial metabolites with relatively high molecular weights and high degrees of aromatization. MBC also significantly increased, and the abundance of beneficial bacteria (<i>Bacillus</i> and <i>Mesobacillus</i>) and microorganisms with the potential for carbon sequestration (<i>Moorella</i>) increased.</p> Conclusions <p>ECM plants can increase the carbon input to coastal saline soils, improve the stability of organic carbon and enrich beneficial bacteria. These findings demonstrate that afforestation via ECM plants is an effective means of improving coastal saline soils for carbon enhancement.</p>