Composite bridge decks consisting of steel plates and concrete are used to minimize fatigue cracking and damage of asphalt pavement of orthotropic steel bridge decks subjected to wheel loads. This paper presents a methodology to optimize the parameters and mechanical performance of a corrugated steel plate-ultrahigh-performance concrete (UHPC) composite bridge deck with panel zone (PZ) shear connectors using the improved non-dominated sorting genetic algorithm (NSGA-II). A 3-D finite element model is established in ANSYS Workbench software to conduct numerical parameter analysis, and ABAQUS software is used to analyze the optimized model’s mechanical performance. The results show a significant improvement in the mechanical performance of the optimized composite bridge deck, with a 27.66% decrease in the maximum stress in the UHPC layer. The vertical displacement of the optimized composite bridge deck increases sharply when the load reaches 90% of the ultimate load, and a significant change in the strain is caused by the sliding displacement between the UHPC layer and steel plate. The bottom part of the corrugation yields first in the middle span, followed by failures of the ribs. In addition, as the tensile stress increases, damage occurs first in the UHPC layer near the PZ shear connectors in the shear bending area and the bottom in the bending area, expanding significantly to the entire bending and loading areas. The results indicate that the parameter optimization of the corrugated steel plate-UHPC composite bridge deck using NSGA-II improves the structure’s bending performance.