Based on the analysis of the plasma physics mechanism in negative hydrogen ion source, the particle-in-cell algorithm is studied and optimized and a high efficient storage method of particles is designed. Using the Monte Carlo collision model, considering the plasma potential and coulomb collisions between charged particles, the full three-dimensional particle-in-cell/ Monte Carlo algorithm (PIC/MCC) is developed. With the magnetic charge model, using the FDTD method, the line cusp magnetic field is calculated. With the negative hydrogen ion source JT-60U and considering the main reactions in the negative hydrogen ion source, the full three-dimensional PIC/MCC simulation algorithm is verified by simulation.