Elevated mineral fertilization may change the composition and increase the availability of soil phosphorus (P) in subtropical paddy soils and thus affect long-term plant growth. However, an understanding of the response of soil P fractions to long-term nitrogen, phosphorus and potassium (NPK) additions remains elusive. This study aimed to explore the responses of soil P-fractions and their mobility to different long-term chemical fertilization rates under a double rice cropping system. The rates of nitrogen (N), phosphorus (P), and potassium (K) in the low NPK treatment (LNPK) were 90, 45, and 75 kg ha−1 year−1, respectively, and in the high NPK treatment (HNPK), they were 180, 90, and 150 kg ha−1 year−1, respectively. The results showed that the concentrations of soil organic matter (SOM), total P, Olsen P, total N, and mineral N were remarkably increased under HNPK by 17.46%, 162.66%, 721.16%, 104.42%, and 414.46%, respectively, compared with those under control (CT). Compared to the CT P fractions, HNPK increased the labile P fractions (i.e., NaHCO3-Pi and NaHCO3-Po) by 322.25% and 83.53% and the moderately labile P fractions (i.e., NaOH-Pi, NaOH-Po and HCl. dil. Pi) by 163.54%, 183.78%, and 3167.25% respectively, while the non-labile P was decreased by the HNPK addition. P uptake and grain yield were increased by LNPK and HNPK by 10.02% and 35.20%, respectively, compared with CT. P use efficiency indices were also higher under HNPK than under LNPK. There was a strong positive relationship between grain yield and P use efficiency (R2 = 0.97). A redundancy analysis (RDA) showed a strong correlation between soil chemical properties and the labile and moderately labile P pools. Structural equation modeling (SEM) revealed that SOM, mineral N, and available P strongly control the labile P pool. In conclusion, NPK additions under the paddy soils significantly influences the soil P fractions. The soil P dynamics and the mechanisms governing the interactions between plants and soil nutrients are clearly explained in this study.