The negative hydrogen ion source neutral particle transmission characteristics and the physical processes of the negative hydrogen ion extracted from plasma grid surface are analyzed. The influence of the extraction hole transfer rate which leads to hydrogen atom transmission is studied. A physical phenomenon of collision and reflection between H and different attribution conductor walls is explored. Then based on CHIPIC software platform, a full three-dimensional PIC-MCC simulation algorithm, in which the H transmission and the physical process of negative hydrogen ion production can be simulated, is successfully developed. It is verified by the simulation of JAEA 10A model. While the simulation reaches a steady state, the average energy of H is about 0.57 eV and H presents +Y drift. The non-uniform H beam bombarding the extraction wall leads to the spatial nonuniformity of negative hydrogen ions. These simulation results are consistent with those given in the literature, thereby verifying the reliability of the algorithm.