Small scale high-voltage flyback charging circuit is the key unit of the initiating experiment device of slapper detonator, which converts the initiating energy from low voltage to high voltage and stores the energy in a high voltage capacitor. It is a highly nonlinear system, of which the research topic is the process of the establishment of the output voltage—an area which belongs to large signal transients. This has made the research of this topic difficult and progress slowly. In this paper, in order to study the characteristics as well as the rules of the charging process for the purpose of design optimization, the discrete time domain model of the flyback charging circuit is built and simulated. Experimental results are given and show that the model presented in this paper is instrumental for the optimization of the high voltage charging circuit.