The aim of this study was to investigate the effects of manipulated organic matter input (root exclusion, litter removal, and control) on the soil carbon (C) and nitrogen (N) pools in three plantation forests growing on the coastal sandy soil in Changle City, Fujian Province, China. Three plantations included Eucalyptus urophylla×E. grandis hybrid, Acacia aulacocarpa,and Casuarina equisetifolia. The soil C and N stocks, dissolved organic carbon (DOC) and nitrogen (DON) concentrations, and microbial biomass carbon (MBC) and nitrogen (MBN) concentrations were measured after one year of organic matter treatment. The results showed no significant difference in the soil C and N stocks among the three plantations. However, significant difference was observed in the labile carbon and nitrogen components, C. equisetifolia soil showing significantly higher DOC than A. aulacocarpa soil, A. aulacocarpa soil showing significantly higher DON than E. urophylla×E. grandis hybrid and C. equisetifolia soil, and E. urophylla×E. grandis hybrid soil showing significantly higher MBN than A. aulacocarpa and C. equisetifolia soil. Changes in the above-and below-ground C input significantly affected the soil C and N pools, depending on the tree species. Litter removal decreased soil C stocks of A. aulacocarpa and C. equisetifolia by 38.0 and 25.1%, respectively, and the soil N stocks of A. aulacocarpa and C. equisetifolia by 12.9 and 12.5%, respectively. Furthermore, litter removal significantly decreased the soil DOC by 37.5, 30.6, and 52.9; MBC by 31.0, 56.9, and 29.7; and MBN by 50.7, 34.9, 42.2 of E. urophylla×E. grandis hybrids, A. aulacocarpa, and C. equisetifolia, respectively. However, the root exclusion decreased only the soil MBC of E. urophylla×E. grandis hybrids and A. aulacocarpa by 57.7 and 15.4%, respectively. Regression analysis indicated that the soil DOC and MBC were positively correlated with the soil C stocks, while accounting for 47.7% and 57.7% of the variations in soil C stocks. In conclusion, our study suggested that the tree species regulate their soil C and N pools through the effects of the above-and below-ground inputs on soil DOC, DON, MBC and MBN.