The biogeochemical cycle of Si plays an important role in maintaining the function and stability of ecosystems. Although there have been many studies on long-term silicate weathering, there are few reports on Si fractions and cycling in early ecosystem development. Using optimized sequential chemical extraction processes, this study quantified soil Si fractions of the eluvial horizon and deposition layers in Hailuogou Glacier Retreat Area of Gongga Mountain, Southwest China. The results showed that plant-available Si (NaAc-Si) content decreased significantly from 33.40 to 2.16 mg kg −1 with the increase of soil age. There was a significantly positive correlation (p < .01) between soil pH and NaAc-Si. Within the labile Si fractions, the largest fraction was amorphous Si (Na 2 CO 3 -Si) (165.35 ± 81.50 mg kg −1 ), followed by pedogenic oxides/hydroxides chemisorbed Si (Oxalate-Si) (135.13 ± 66.83 mg kg −1 ), Si adsorbed on the surface of inorganic soil particles (Acetic-Si) (9.66 ± 4.27 mg kg −1 ), and soluble Si (CaCl 2 -Si) (4.89 ± 1.68 mg kg −1 ). Compared with Stage 1 (i.e., a variety of pioneer species symbiosis stage) after glacier retreat, the storage of these four labile Si fractions in Stage 3 (i.e., climax species stage) decreased by 45.95% (CaCl 2 -Si), 42.98% (Acetic-Si), 67.34% (Oxalate-Si), and 75.24% (Na 2 CO 3 -Si), respectively, due to the absorption and utilization of Si by plants. Our study implies that the multiple transformations of different Si fractions in soils and the absorption and return of Si by plants can keep the CaCl 2 -Si pool in dynamic equilibrium, which provides a basis for the stability of ecosystem functions during the vegetation evolution after glacier retreat.