In this paper, in order to improve the control characteristics of the centrifugal pump flow control system, a mathematical model of the centrifugal pump flow control system was established based on an analysis of the basic structures, such as the frequency converter, motor, and centrifugal pump. Based on the adaptive control theory, the recursive least squares algorithm with a forgetting factor was used to estimate the real-time parameters of the centrifugal pump control system, and the self-tuning PID control method was used to optimize the mathematical model of the centrifugal pump flow control system. The simulation results showed that the adjustment time of the optimized system was shortened by 16.58%, and the maximum overshoot was reduced by 83.90%, which improved the rapidity and stability of the transient response of the system. This showed that adaptive control had a significant effect on improving the robustness and anti-interference ability of the centrifugal pump control system. In order to further verify the accuracy of the self-tuning PID control method, a flow adaptive control system test platform was built. The test results showed that under the conditions of constant frequency and variable frequency, the actual flow rate of the centrifugal pump was always kept near the set flow rate, the error was small, and it had better real-time followability. The research results showed that adaptive control could revise the parameters in real-time according to changes to the centrifugal pump control system, which improved the stability and robustness of the system. Therefore, adaptive PID control could effectively improve the adaptability of centrifugal pumps to various complex working conditions and improve the working efficiency of centrifugal pumps.