To investigate the effect of functional groups for the organic acid on the crystal transition of phosphogypsum crystals, the adsorption reactions on the surface of CaSO4·05H2O of 3 kinds of organic acid including the succinic acid, the malic acid and the maleic acid was simulated by the computer simulation technology. The priorities of crystallization effect were obtained by the calculation of the adsorption energy of the interaction between the organic acid and the CaSO4·05H2O crystal surface. Comparing the changes of the density of states of carboxyl and the crystal surface, the activation degree of bond length and the angle in carboxyl group, it can be found that introduction of hydroxyl and double bonds to the succinic acid is helpful to enhance the complexing ability of Ca2+ to carboxyl group. The gypsum crystal shapes have been investigated by scanning electron microscope before and after modification along with the measurements of the mechanical properties of phosphogypsum. It can be concluded that the simulation results are consistent with the experimental results well. The maximum compressive strength and flexural strength of the test block treated by the malic acid are 1285 Mpa and 421MPa, respectively.