Couples in consanguineous unions share varying proportions of genes, leading to increased autozygosity and various health outcomes for their offspring. This study investigated the association between consanguinity and mortality at various stages among the progeny of 788 couples in the Chaouia population, Morocco. It was based on part of the data from a survey-based cross-sectional study conducted between January 2019 and January 2020. Our findings revealed higher mortality rates in children from consanguineous marriages compared to those from non-consanguineous ones. The univariate logistic regression analysis unveiled a significant association between neonatal (OR = 3.7; p = 0.001), infant (OR = 2.31; p = 0.008), and under-5 (U5) mortality (OR = 1.94; p = 0.03), particularly among male offspring (OR = 2.38; p = 0.01), born from marriages between cousins with a high coefficient of consanguinity (F > =0.0625). Post-neonatal mortality and mortality in female offspring showed no association with consanguinity. After adjusting for relevant socio-demographic factors in multivariate analysis, the significant association between consanguinity and mortality persisted in neonatal and infant stages, as well as among males. However, it did not maintain statistical significance for U5 mortality. Additionally, mortality, regardless of age at death, significantly correlated with a higher number of live births per couple. These findings highlight the importance of considering socio-demographic factors while assessing the complex relationship between consanguinity and mortality. These insights are critical for directing future public health interventions to enhance child health and well-being.