Abstract: By the theoretical analysis of the Miniature Neutron Source Reactor (MNSR) control system, the corresponding Simulink model was established and the simulation analysis of the MNSR control system was carried out. To facilitate the stability analysis, the mathematical model of the MNSR control system was reduced and discretized, based on the open-loop transfer function after reduction and discretization, the stability analysis was performed using the rltool analysis toolbox of the Matlab, and the critical gain for different sampling time was obtained. The calibration of the proportional coefficient K_p for the PID controller at different sampling time Ts was carried out with the introduction of positive step reactivity in the steady-state operation of the reactor, and the optimal calibration values of K_p at different sampling time were determined. The optimal differential coefficient K_d at different T_s and K_p was calibrated. After calibrations of T_s, K_p and K_d, the reactor neutron flux density, control rod velocity and response to control rod introduction reactivity at negative step reactivity input and slope reactivity input were analyzed at T_s=60 ms, K_p=2 500 and K_d=300. The results of the simulation analysis show that the Simulink modeling about the MNSR control system is accurate and the analytical data are reliable, which provides a theoretical basis for software and hardware designs of the MNSR control system.