One of the most unfavorable problems of orthotropic steel deck (OSD) is the penetrating crack on rib-to-deck welded joints, which may reduce the local stiffness that harms bridge serviceability by introducing premature pavement damages and consequent corrosions on the top of the deck. In this study, it is suggested to retrofit cracked OSDs by bonding a structural layer made by methyl methacrylate mortar (MMA). The fatigue tests are designed and implemented, consisting of three phases: I) pre-cracking; II) fatigue crack growth; III) failure. During the test, the fatigue crack initiates on the rib-to-deck weld root of OSD specimens and grows towards penetrating the deck in Phase I. By bonding a MMA layer on a specimen in Phase II, the crack growth rate is reduced prominently. In Phase III, the fatigue load can be increased to show the failure modes. The failure analyses on specimens are conducted with emphases on the crack growth process, showing that the crack growth rate is significantly slowed down in Phase II. The finite element analysis is further performed for typical cracks on specimens, indicating a reduction of stress intensity factors of about 44%. It can be inferred that, when a MMA layer is paved on the deck of OSDs, the fatigue crack growth rate of the penetrating crack can be reduced to a satisfactory degree, even if the interface between the OSD and the MMA do not form a perfect composite system. Therefore, the study can provide an alternative strategy in fatigue retrofitting works of OSDs, which benefits the bridge maintenances during its life cycle.