As ultra-high performance concrete (UHPC) has superior mechanical and durability properties, it is a promising solution to apply a thin layer of UHPC on top of normal concrete bridge decks to extend the service life and enhance the structure integrity. However, the large autogenous shrinkage characteristics of UHPC is still an issue, and there is a lack of research focus on the structural design and stress analysis of the concrete bridge deck and UHPC overlay system. Thus, this study first designs and evaluates a new low-shrinkage UHPC mixture internally cured with a high-strength, high-abrasion resistant, and porous aggregate (calcined bauxite, CB), and the optical mixture design is validated by testing the fresh, mechanical, autogenous shrinkage, abrasion, and impact properties of the UHPCs. Second, the outdoor UHPC overlay-NC composite slab experiments and the numerical modeling are carried out to analyze the shrinkage performance of the UHPC, debonding potential of the overlay layer, stress and strains development in the system. Then, the significant influencing factors and the key measures to assure the UHPC-NC interface bonding properties are obtained, including proposing a grouped L-shape steel rebar arrangement for strengthening the interface. Finally, the applicability of the new low-shrinkage UHPC mixture as overlay materials on a real concrete bridge deck is demonstrated. Based on these, the engineering design scheme and the construction recommendations of an environmentally-cured low-shrinkage UHPC overlay on concrete bridge deck is given. The utilization of UHPC overlay on concrete bridge decks offers a novel paving system that substantially enhances strength, abrasion resistance, and durability.