In order to explore the possibility of using FGD gypsum in controlling P loss due to agricultural runoff, the effects of FGD gypsum on the P fraction were studied in the Yangtze River Delta coastal plains. The field experiments were conducted to identify (1) different application rates of FGD Gypsum to the P losses and (2) formation of Ca-P complexes in the soil in response to FGD gypsum applications. The field experiments consisted four rates of FGD gypsum (0, 15, 30, and 45 t/ha) in triplicate. FGD gypsum was obtained from a coal burning power plant. The “S” multi-point sampling method was used to collect samples of the uppermost soil interval in July and December of 2015. The total phosphorus (TP) in soil and plants was determined using the sulfuric acid-perchloric acid digestion method. The available phosphorus (AP) was determined using the sodium bicarbonate extraction-molybdenum-antimony anti-spectrophotometric method. The soluble reactive phosphorus (SRP) in the soil leachate was determined using the molybdenum-antimony anti-spectrophotometric method. The Visual MINTEQ 3.0 model was used to simulate the forms and distribution of the P fractions in the soil solution. The results indicated that the soil P fractions changed with application rats of FGD gypsum while the total soil P showed no significant change. The concentrations of SRP in the leachate also decreased in average of 27.5, 41.9, and 54.5%, respectively, with increasing FGD gypsum rates. The amounts of Ca2-P, Ca8-P, and Ca10-P of the calcium phosphates in the soil were significantly increased over the ranges of 44.3–68.6, 34.1–70.1, and 7.4–17.2%, while soil AP concentrations decreased. Visual MINTEQ modeling confirmed the speciation and fractionation of Ca-P compounds under the coastal plain soil conditions. The field experiments also showed that FGD gypsum applications did not affect the absorption of P by the vegetation. Experiments indicated that FGD gypsum has been shown to react with P in soil, resulting in decrease of AP and SRP and formation of insoluble Ca-P compounds and thereby decreasing the potential of P losses with surface runoff. FGD gypsum appears to be a more viable soil amendment than commercially mined gypsum to potentially achieve reductions in P losses and eutrophication of receiving waters.