Segment lifting, performed by an electro-hydraulic system including two cylinders, is a crucial step in segment grasping, transporting, and assembly in tunnel boring machines. Due to heavy and uneven loading, large vibration, uncertainty of parameters, and nonlinear friction, it is difficult to develop an accurate physical model. This paper presents a comprehensive procedure to achieve two-cylinder automation and synchronisation according to the actual engineering requirements and environments. An improved deviation compensation recursive least squares identification algorithm with a forgetting factor was used to identify the key parameters of the model. To achieve synchronous control and precise control of the lifting system, SMC with improved sliding mode approach rate and the deviation coupling method of fusion single neuron PID were designed and verified by simulation. A full-scale bench test was also performed to show that the tracking steady-state error is below 4 mm, and the synchronisation error is below 2 mm.