Ultrahigh-performance concrete-orthotropic steel composite bridge deck is composed of the orthotropic steel deck and a thin ultrahigh-performance concrete (UHPC) overlayer. In the previous fatigue tests, two typical fatigue failure modes were found and identified. As a supplementary test after fatigue tests, air penetration method is capable of providing a reference to the quantitative and non-destructive damage detection of fatigue damage of UHPC. To further the previous study, a detailed numerical investigation is accomplished through complimentary finite element (FE) analysis. Compared with the solid element model, the refined shell-solid element model can better reflect the mechanical behavior. It is illustrated that the vertical stress can be adopted in assessing the fatigue strength of rib-to-diaphragm welded connection in the field test by means of nominal stress method. The combination of various factors would lead to fatigue shear failure of the short headed-studs. The fatigue strength of rib-to-diaphragm welded connection predicted by the hot spot stress method and the consistent nominal stress (CNS) method can basically meet the requirements of FAT90. The consistent nominal stress method can be used as the optimization method of nominal stress of fatigue detail. It is demonstrated that the fatigue life of UHPC can be estimated by S-N curves of ordinary concrete conservatively. The allowable equivalent maximum stress level can be taken as 0.55 for two million cycles of fatigue loading, and 0.52 for five million cycles of fatigue loading.