Circuit tolerance design for circuit systems is an important technology for system reliability analysis, it can make the output of the circuit stably and reliable. Being one important part of high power laser facility, power conditioning system should be designed with high reliability. Circuit tolerance design of power conditioning system is an important part of reliability analysis of high power laser facility. In this paper, the function and circuit diagram of power conditioning system are presented. Then based on the general model of circuit tolerance design, by the use of stochastic optimizing design method, a mathematical model is set up which will be used in the tolerance analysis of power condition system circuit and explain the design variable, random parameter, design rule and constraint of the model. In the end, the flow chart of computer simulation solution for stochastic optimizing model and the set of feasible result are represented.