The numerical simulation of the beam transmission efficiency dependent on the charge exchange of accelerated ions with the residual gas has been carried out for the CI-100 cyclotron and its subsystems: the axial injection system and the extracted beam channel. The CI-100 cyclotron, used for applied physics researches, will be equipped with an ECR ion source. Produced modeling calculations allow determining the main requirements for the basic parameters of the vacuum system in order to provide the necessary transmission efficiency of accelerated heavy ions.