In this study, an orthotropic steel bridge deck overlaid with ultra-high-performance fiber-reinforced concrete (UHPFRC) is investigated using the finite element analysis. The composite bridge deck which is undergone moving-wheel load is examined under environmental surface water conditions. Two phases, i.e., Phases 1 and 2, are considered for the material model of the UHPFRC with stagnant water. In Phase 1, mechanical recoveries of the tensile strength and reloading stiffness are considered for the cracked UHPFRC caused by the autogenous self-healing behavior. In Phase 2, under the moving-wheel load, the crack bridging stress degradation in reinforced overlayer accelerates due to the closing–opening actions of surface cracks in water. In both phases, the deformation behaviors of the steel deck plate and UHPFRC overlayer are numerically examined. The results of the current numerical model agree with the experimental data in terms of the strain tendency, wherein the strain range of the steel deck plate and UHPFRC overlayer decreases in Phase 1 and progressively increases in Phase 2. Therefore, it can be asserted that, under the surface water condition, scenarios considering two phases of the material model of cracked UHPFRC, have governed the strain behaviors of the tested composite bridge deck.