Congenital anomalies remain an important cause of childhood mortality in China. We examined national mortality trends, the contributions of population age structure and age-specific mortality, and changes in geographical inequalities from 2008 to 2021. We analyzed aggregate data from the China Cause of Death Surveillance System using Joinpoint regression, sensitivity analyses addressing the 2013 surveillance expansion, generalized additive models, and symmetric two-factor Das Gupta decomposition. We assessed inequalities among children younger than five years using the slope index of inequality (SII) and relative index of inequality (RII). Deterministic bias analyses examined fixed and changing patterns of residual ascertainment. The national age-standardized mortality rate declined from 2.90 to 1.11 per 100,000 population (average annual percentage change, − 6.54%; 95% confidence interval [CI], − 8.74% to − 4.29%). Analyses addressing the surveillance transition also indicated a decline. Population age structure and age-specific mortality contributed − 0.23 and − 1.54 deaths per 100,000, respectively, to the change in crude mortality. For circulatory anomalies among children younger than five years, regional SII decreased from 8.36 to 7.05, whereas RII increased from 1.42 to 4.25. Assuming a 30% residual ascertainment deficit at the disadvantaged rank endpoint in 2009 and no deficit in 2021, the 2021 RII for circulatory anomalies remained 2.10 times the 2009 value. Urban–rural SII was significantly negative during 2013–2018. Assuming 20% additional rural under-ascertainment changed the 2015 RII from 0.62 to 0.97 (conditional 95% CI, 0.83 to 1.12). Congenital anomaly mortality declined, while relative regional inequalities increased for several cause groups. The increase in regional relative inequality persisted under scenarios assuming an initial 10–30% residual ascertainment deficit in 2009 that disappeared by 2021, although larger initial deficits could eliminate the increase. The urban–rural reversal was more sensitive to differential ascertainment.
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