A state estimation controller for double input and double output liquid level control system was designed. The structure and working principle of the double input and double output liquid level control system were studied. On the basis of considering the centralized disturbance of the system, the state space equation of the system was obtained by using the known gain delay ratio of the system. The linear extended state observer was used to construct the estimation equation of the system, and the state estimation controller was constructed by using the proportional value of the error between the expected signal and the output signal. Through the designed state estimation controller, the estimation equations and control signals of the two channels in the dual input and dual output liquid level system were obtained. The disturbance observer method was introduced into the experiment to track the constant and changing desired liquid level curves. The results show that when tracking the constant and changing liquid level curve, by using the proposed method, the double input and double output liquid level control system can be controlled better, the system liquid level can be controlld to change rapidly according to the expected liquid level, and the accurate control of the double input and double output liquid level control can be realized.