While the global phosphorus (P) resources is running low, the environmental issues due to over-application of P fertilizers become increasingly urgent. There is a more pressing need than ever before to develop new types of P fertilizers with high phytoavailability with agronomic, environmental and sustainability benefits. Compared to generally applied inorganic P fertilizers, organically bound P fertilizers are less prone to soil fixation, and could remain relatively high mobility from where the fertilizer is added to the rhizosphere for crop utilization. Developing organically bound P fertilizers is increasingly recognized as an efficient way to fundamentally solve the current problem induced by the low phytoavailability of inorganic P fertilizers. In recent few years, related studies are becoming popular, but researches on the speciation of the emerging organically bound P fertilizers are not well-documented until now. Various organically bound P fertilizers were developed and their P phytoavailability were tested. Our previous study showed that the starch-bound P fertilizer had high P efficiency. Since the phytoavailability of P fertilizers was a function of the P species present in the fertilizer and the transformations in soils after application, this current study probed P speciation in the starch-bound P fertilizer at the molecular level by solution P-31 nuclear magnetic resonance (P-NMR) and synchrotron-based X-ray absorption near-edge structure (XANES) spectroscopy. To obtain quantitative results by P-NMR analysis, the fertilizer sample was hydrolyzed to α-limited dextrin, and then dissolved with dimethyl sulfoxide solution (45%). Nicotinamide adenine dinucleotide was added as an internal reference standard. It indicated that the total P concentration in the studied fertilizer by NMR agreed with that by the colorimetric chemical method. Phosphorus in the starch-bound P fertilizer was mainly presented as orthophosphate monoester, representing 75.8% of total P. Orthophosphate diester accounted for 17.3% of total P, while inorganic P only 6.9%. Furthermore, the XANES spectra of the P fertilizer closely resembled that of phytic acid, and was lack of the characteristic features of inorganic P species. Conclusively, these results illustrated the dominance of organic orthophosphate monoester in the studied fertilizer. Combining state-of-the-art of spectroscopic analysis, this study provides an important basis for further studies on the high phytoavailability mechanisms of organically bound P fertilizers.