As a new dynamic density functional method, the mesoscopic dynamics (MesoDyn) is used to simulate the microphase separation of the binary mixture of tri-block copolymer P123 ((EO)(20)(PO)(70)(EO)(20)) and water. With a simple copolymer model, various aggregate structures of P 123 in water including the micelle, hexagonal, and lamellar phases are produced, which can partly reproduce most experimental phase regions. The simulated phase ranges are more or less different from those established from experiment, especially at high polymer concentrations. This can be attributed to different phase mapping situations, that is, the constant shear used in simulation versus the varied external forces in experiment. The calculated trend for micelle size change in diluted region is co-incident well with previous observations in other Pluronic systems. The poly(propylene oxide) (PO) block amount is found to influence not only the aggregate morphology but also its formation rate in solution. Obtained results indicate that the mesoscopic simulation is a valuable tool to supplement the experimental study on aggregates formation.