To evaluate time trends of exomphalos prevalence using a large population-based study with cases identified by the Liaoning Birth Defects Registry including 14 cities over the course of a 10-year period. Exomphalos prevalence, percent change, annual percent change (APC), and contribution rates of each city were calculated. Additionally, epidemiological characteristics of this malformation were described. We observed 516 cases of exomphalos among 3,248,954 live births. Birth prevalence of exomphalos was 1.59 per 10,000 live births with non-significant change during the observational period (APC = −1.19%, P = 0.48). However, significantly decreasing trends were noticed in three cities: Fushun (APC = −9.15%, P = 0.03), Benxi (APC = −11.49%, P = 0.05), and Yingkou (APC = −16.47%, P = 0.04), contributing 62.77% of the decreasing trend of overall prevalence. The mean maternal age, gestational age, and birth weight was 28.4 years (standard deviation [SD], 6.1 years), 25.6 weeks (SD, 8.6 weeks), and 1236.2 gram (SD, 1164.4 gram). For time of diagnosis, 79.8% (n = 412) cases were diagnosed during pregnancy. In summary, the prevalence of exomphalos in Liaoning province did not change remarkably during 2006 to 2015. Future studies are warranted to investigate the risk factors and create prevention strategies for this disease.