Rail-cum-road truss bridges are rapidly developing, and frequent cracking in freshly poured concrete is of great concern. For the performance of such a load-bearing deck, it is necessary to understand its stress status due to short-term shrinkage. In this study, a newly constructed railway-cum-highway truss bridge in Guangdong Province was used to analyze the stress distribution in the concrete deck under short-term shrinkage. In-situ tests were performed to measure the shrinkage of one deck panel and two companion specimens shortly after the concrete pouring. It was found that the free shrinkage of companion specimens at 42 days was 140–150 microstrains, which was significantly higher than that indicated by current codes or standards. An exponential form of shrinkage development curve was proposed based on shrinkage test results. The measured shrinkage of the deck panel varied with locations, with a relatively large concrete shrinkage between grillages, reaching 45–55 microstrains at the end of the shrinkage test. The resulting mechanical strain due to restraints, taken as the difference in measured strains between the deck panel and companion specimen, was consistent with numerical simulation results, demonstrating the validity of the analysis method adopted. Under short-term shrinkage, the secondary tensile stress of 1.5–3.5 MPa was present in the deck above the main trusses and cross beams, triggering potential cracking. The stress is primarily attributed to the external restraint from connecting steel members, whose degree of restraint dramatically exceeds that of internal restraint from reinforcement. Although creep tends to reduce such shrinkage stress slightly, the effect of short-term shrinkage requires significant attention.