Forest ecosystem has the function of carbon sequestration, and effective management is essential to increase its carbon density. However, as rural labor transferred, the level of forest management changed accordingly, which in turn affected the carbon density of forest ecosystem. It is necessary to clarify such influencing mechanism so as to maintain the high carbon density. Thus, based on the official forestry survey data and questionnaire survey data of 253 villages in five counties (districts) of Fujian Province from 1999 to 2009, this paper evaluated the forest carbon density by adopting the conversion factor continuous function method. Then hierarchical regression model was developed to analyze the effect of labor transfer on forest carbon density, and to verify the mediating effect of forest management. The results showed that:(1) The forest carbon density in the sample area generally showed an upward trend in the past 10 years, but presented significant regional differences in space. The forest carbon density increased from south to north, while the lifting rate decreased from south to north. (2) Forest carbon density is significantly promoted by the labor transfer and weakened by forest management, where forest management exerted a significant mediating effect on the relationship between labor transfer and forest carbon density. That is, the labor transfer can ultimately promote the increase of forest carbon density through weakening the level of forest management and reducing the human disturbance. (3) Factors including labor characteristics, harvesting methods and natural forest endowments have significant impacts on forest carbon density. Specifically, the higher the average age of the labor force engaged in forestry production in the village, the higher the forest carbon density. It is related to the reduced dependence on forest livelihoods as the workforce ages. The proportion of harvesting has a significant positive effect on the increase of forest carbon density, due to the benefits from appropriate harvesting to the stock volume and the regeneration of understory vegetation. Natural forest origin positively affects the carbon density, attributed to its abundance in tree species and better function of carbon sequestration. Single tree species negatively impact the forest carbon density, which conversely proves that richer forest tree species contribute to overall carbon density increase. To this end, suggestions are proposed as follows:appropriately reducing the artificial interference to forest ecosystem, enriching livelihood sources of foresters, transforming the objectives of forestry management, scientifically harvesting the mature and overripe forests, protecting natural origin forests, and enriching plantation tree species.