Purpose Polyphosphate (Poly-P) is an alternative source of phosphate (P) fertilizer. However, as a condensed P, the effects of different polymerization content of poly-P on crop P nutrition status are often inconsistent. The aims of this study are to explore the transformation of fraction and the fate of poly-P in calcareous soils with ammonium polyphosphate (APP) of different polymerization content as P resource that reveal the effects of different polymerization content of poly-P fertilizer on maize growth (Zea mays L.), soil available P, Fe, Zn, and Mn, and soil inorganic P transformation. Materials and methods A pot experiment was carried out with four treatments: (i) no phosphate fertilizer (control); (ii) mono-ammonium phosphate (MAP); (iii) APP with averaging polymerization degrees of 3 and poly-P/total-P of 70% (APP-3-70%); (iv) APP with averaging polymerization degrees of 3.8 and poly-P/total-P of 90% (APP-3.8-90%). Concentrations of soil available Fe, Zn, and Mn were determined by inductively coupled plasma-atomic absorption spectroscopy procedure. Soil inorganic P species were determined by sequential extraction method. Results and discussion Compared with the MAP treatment, soil available P, Fe, and Zn concentrations significantly increased by 22.7%, 6.5%, and 16.7% respectively, in the APP-3.8-90% treatment. Soil labile P forms of resin-P, NaHCO3-P and NaOH-P in the APP-3.8-90% treatment were 91.6%, 24.4% and 27.6% higher, respectively, relative to the MAP treatment, while soil HCl-P concentration was decreased by 7.2%, accordingly. Maize seedling total dry weight (shoot plus root) in the APP-3.8-90% treatment was 42.4% higher than in the MAP treatment. In addition, the APP-3.8-90% treatment is more pronounced than the APP-3-70% treatment in increasing soil available P and Fe, Mn, and Zn. Conclusions Poly-P application exhibited obvious advantages in increasing soil P availability and mobilizing soil micronutrients. Specially, appropriately increasing the polymerization content of poly-P is beneficial to play a better role. Hence, it could be recommended as a promising source of P fertilizer substituting orthophosphate (ortho-P) fertilizers.