At present, the controllable parameters of micro turbojet engines in engineering applications are mainly speed-fuel flow (hereinafter referred to as flow) control, in which closed-loop proportional–integral–derivative (PID) control is mostly used to achieve a stable control of engine speed under slow engine conditions. For the optimal adjustment of PID parameters, this paper designs an improved evolutionary strategy for the self-tuning of control parameters in the engine speed and flow control system and formulates an improved PI controller based on a neural network. The simulation experimental results show that the method can realistically achieve stable and fast control of the engine under above slow conditions.