Based on GEANT4 simulation, a feasible numerical simulation method is provided for the beam dynamics design of cyclotron. Through the electromagnetic field simulation software Opera, the corresponding electromagnetic field data are imported into GEANT4 for interpolation calculation. The equilibrium orbit, oscillation frequency and acceleration orbit of particles are calculated by using the electromagnetic field differential equation and differential equation solver of GEANT4. The results show that: for the transverse motion, GEANT4 calculation results and the traditional numerical method calculation results tend to be consistent; for the axial motion, due to the difference of the magnetic field interpolation method, there is a certain difference between the two. For the acceleration of the non-equilibrium particle, its energy changes around the equilibrium particle. For the beam loss, the simulation is closer to the actual experimental situation by limiting the particle motion time, accelerating the calculation efficiency by axial displacement and adding the determination of electrode collision.