Prefabricated lining is increasingly used in railway tunnels due to its advantages of environmental friendliness, high construction efficiency, and convenience. However, the existence of block joints weakens structural integrity, and the segmentation optimization of prefabricated lining remains a challenge especially for irregular lining. Based on the Yongfengcun tunnel in the Fuzhou Ganghou Railway Project, the nonlinear mechanical behaviors of joint stiffness were investigated under axial force, bending moment and shear force. A beam–spring model was established by considering the bending and shearing stiffness of block joints, and the mechanical behaviors were analyzed efficiently by Python 3.9 and ABAQUS 2025 for 572 segmentation schemes. Based on a Delphi questionnaire, three key indicators including horizontal convergence, bending moment amplitude and length variance were selected as independent optimization objectives. The stable Pareto frontier was obtained using the NSGA-II algorithm. Application in the Yongfengcun tunnel fully verified the effectiveness of the method.