Despite the abundant content of soil total phosphorus, it is a key limiting factor of primary productivity in most terrestrial ecosystems, owing to low weathering rate of parent materials, leaching and its strong affinity to soil minerals. Currently, it remains largely unknown about how soil phosphorus fraction changes with increasing stand age of Cryptomeria japonica var. sinensis and its relationship with soil microbial communities. This study aims to explore the variation patterns of soil phosphorus fractions in C. japonica plantations with different stand ages and soil depths, and to address the relationships between soil microbial communities and different soil phosphorus fractions. This study was conducted in rainy area of western China, soil samples from different stand ages of C. japonica plantations (7-year-old young forest, 13-year-old middle-aged forest, 24-year-old near-mature forest, 33-year-old mature forest and 53-year-old over-mature forest) were collected. Using Hedley's sequential P fractionation and phospholipid fatty acids (PLFA) methods, the above goals were achieved. The results showed that each fraction of soil P was significantly different among stand ages and soil depths. With the growth of C. japonica, the content of soluble organic phosphorus (Soluble P_i) and apatite phosphate (Dil.HCl-P_i) gradually decreased, and the content of residual phosphorus (Residual P) gradually increased, and the content of other phosphorus fractions showed increasing firstly and then decreasing trends. Except for the Soluble P_i, Conc.HCl-P_i and Residual P, all soil phosphorus fractions were significantly different regarding different soil depths. Under different stand ages, the contents of phosphorus fractions in 0-15 cm soil were significantly higher than those in 15-30 cm soil. Partial Mantel tests showed a significant association between soil microbial communities (represented by phospholipid fatty acids) and soil phosphorus fractions. Further regression analysis showed that soil organic C to total organic P ratio was positively correlated with acid phosphatase activity, which played an important role in obtaining available phosphorus in phosphorus-deficient soil. Redundancy analysis showed that pH, soil organic matter, soil water content, total nitrogen, and soil bulk density were the dominant factors affecting the changes of soil phosphorus fractions. In conclusion, the soil phosphorus fractions in the early stage of afforestation accumulated rapidly, reaching the maximum value in the middle-aged forest stage. With the increase of the stand age of willow fir plantations, a growing intensity of soil phosphorus deficiency was observed. The soil phosphorus fraction content gradually decreased after mature forest. This study provided theoretic bases for the cultivation and sustainable management of C. japonica.