In the paper the algorithm is proposed for the numerical simulation of the thermal conductivity for the design and optimization of cryogenic cells pulsed (in the millisecond range) feeding the working gases into the electron-stringed source of multiply charged ions. Heating process comes when the electric current passed through one of the layer. A model of the cryogenic cell with four layers (materials) is investigated. The heat transfer into the object is described by the system of heat equations with temperature dependent discontinuous thermal coefifcients. The discontinuous thermal coefifcients are given by experimental data and approximated by the least-squares method using the polynomial analytical functions. Conjugation condition between materials is considered to be ideal. The results are reported for a common configuration of the cell. The parallel algorithm for modeling thermal processes into four layer model was developed and speedup of the algorithm in depending on number of CPUs is shown.