Polyelectrolyte brushes grafted on a pair of parallel nanochannel walls can affect the electroosmotic flow (EOF) significantly. A molecular dynamics simulation method is used to investigate the relationship between charge distribution on polyelectrolyte brushes and EOF parameters such as flux, velocity, and density of particles. The EOF can be modulated by changing the step between two charged beads on the same chain, Sc, and the valence of a bead, Nc. Simulation results indicate that the flux increases as the total number of charges on the brushes increases. The decrease of Sc and Nc can lead to a maximum average velocity in the center region. The influence on density of particles is also analyzed.