With the improvement of aquatic trophic level, phytoplankton proliferates rapidly, and a large amount of algae debris finally settled on the surface of sediments. Priming effect would occur on the sediment organic matter (SOM) due to the deposition of algae debris, a fresh labile organic matter, which would affect the cycling process of carbon in sediments. In the current study, the sediments in the southern lake center of Lake Fuxian, the second deepest lake in China, was selected as the research object, and the dominant species Aphanizomenon flos-aquae in Lake Fuxian was chosen to carry out the cultivation experiments with different concentrations of algae debris (×1, ×5 and ×10 treatments). The carbon isotope on-line monitor was conducted to explore the priming effect of algae debris on SOM mineralization and to predict the possible environmental influence. The results revealed that: (1) the addition of algae debris increased the concentrations of CDOM, and influenced the compositions and properties of chromophoric dissolved organic matter (CDOM) in both overlying water and porewater of sediments. It significantly increased the content of protein-like components in CDOM at the earlier stage, and the humification degree of CDOM at the later stage. The addition of algae debris increased the release of CO₂ and the activity of proteinase and invertase simultaneously as well; (2) different levels of priming effect were detected in the algae debris addition treatments. The positive priming effect on the SOM mineralization was found in ×1 and ×5 treatments at the early stage, and then turned into negative excitation effect afterwards, with the highest priming effects of (12.18±0.65) and (26.60±9.14) μg/(mL ws), respectively, while the negative priming effect was shown in ×10 treatment during the whole experiment; (3) the addition of algae debris improved the enrichment of Fe²⁺ and S^2- in porewater and inhibited the denitrification rate, of sediments, which helps to enrich NO₃^-. The activity of alkaline phosphatase in sediments increased due to the addition of algae debris, which indicated the release of reactive phosphorus. It suggested that the addition of algae debris would increase the eutrophication and the risk of black bloom in Lake Fuxian. Therefore, the systematically study of the influence of labile organic matter inputs on SOM biogeochemical process could provide theoretical basis for protecting the water quality of Lake Fuxian.