For the orthotropic steel-ultra high performance concrete (UHPC) composite bridge deck, the early shrinkage of UHPC is relatively large. Under the constraint of the interface of the composite deck, high-order internal forces can be generated, and there is a risk of cracking, thus endangering the safety and durability of the structure. On the basis of the actual engineering background, the shrinkage effect of the composite bridge deck with wet joints was monitored for 90 d under normal temperature curing in natural environment. The development and distribution of UHPC shrinkage of composite bridge deck and the induced secondary internal force were investigated, and the influence of age difference on the development of the shrinkage effect of wet joint area was explored. The finite element model of plate and shell was established, and the shrinkage effect before and after the wet joint pouring of composite bridge deck was simulated by linear superposition of multiple models. Test and finite element analysis results showed that under hot and humid curing environment, the shrinkage development of UHPC experienced four stages: early expansion, rapid shrinkage after initial setting and hardening, slow shrinkage, and stability. The initial setting and hardening of UHPC occurred about 6 h after pouring. Taking the strain at this moment as the reference, the measured shrinkage of UHPC for the first 72 h was about 700×10^-6, and the maximum compressive strain of the steel deck flange measured during this period was about 78×10^-6. UHPC shrinkage was larger in the area near the edge of the bridge deck and smaller in the area near the center of the deck. The shrinkage measured at the wet joint after initial setting and hardening was smaller than that in the surrounding area. The wet joint was well connected with the surrounding area, and the UHPC tensile stress caused by shrinkage tended to increase near the wet joint. The research results can accumulate monitoring data and foundation for the study of shrinkage of composite bridge deck with wet joints.