A 4-year field trial with three treatments and three types of annually rotated vegetables was conducted in calcareous soil in a greenhouse using a phosphorus (P) fractionation method based on the inorganic P fraction classification system described by Jiang-Gu. With the same nutrient input, vegetable yields and P uptake were more stable under the chemical fertilizer (CF) treatment than under the organic manure (OM) treatment, and the average utilization rate of P fertilizer (URP) values were 5.27% and 11.40% under the OM and CF treatments, respectively, over the 4 years. Compared with the values in 2009, the values of the inorganic P (Pi) fractionation, including Ca-P, Al-P and Fe-P, significantly increased over time by 310.89 mg·kg-1, 36.21 mg·kg-1, and 18.77 mg·kg-1, respectively, with OM treatment and by 86.92 mg·kg-1, 175.87 mg·kg-1, and 24.27 mg·kg-1 with CF treatment. These results suggest that 1) large amounts of P were released from Ca2-P, Ca8-P and Al-P and were taken up by vegetables in the calcareous soil, and 2) the excessive application of P fertilizer, especially OM, resulted in a substantial accumulation of Pi (Ca2-P, Ca8-P and Al-P), which increased the risk of pollution from organic farming diffusing into the surface water.