When the hydrogen atom beam is transmitted in the atmosphere, the atmospheric stripping effect formed by the collision ionization between the beam particles and the atmospheric particles and the self-stripping effect formed by the collision ionization with the atmospheric particles are the important mechanisms causing the energy loss of the hydrogen atom beam. Due to the complex causes of self-stripping effect, although there are some theoretical research results, there is no experimental or numerical simulation work on its occurrence mechanism and beam loss effect. Therefore, this paper further improves the theory of self-stripping effect by analyzing the occurrence mechanism of self-stripping effect and its influence on beam loss. On the basis of verifying the applicability of particle cloud grid Monte-Carlo method to the atmospheric transport simulation of hydrogen atom beam through the beam transport equation, the simulation results are compared with the self-stripping theory, which basically verifies the applicability of the self-stripping effect theory. The simulation results show that the self-stripping effect is caused by the charged secondary particle clusters produced by the beam ionization by the atmosphere constantly passing through the beam under the influence of the geomagnetic field, and the strength of the self-stripping effect is related to the density of the atomic beam. The greater the beam density, the stronger the self-stripping effect, and the greater the influence on the beam.