The coexistence of under-nutrition and over-nutrition in developing countries like Ethiopia results in the "mother-child pair double burden of malnutrition," with children experiencing either stunting, wasting or underweight while mothers face overweight or obesity. This poses a major public health challenge, prompting global health organizations to prioritize the issue and urge governments to act quickly. Despite this, there is a lack of research in Ethiopia on the double burden of malnutrition among mother-child pairs at the household level and the factors that worsen it. To assess the magnitude of double burden of malnutrition and its associated factors among mother-child pair at household level in East Ethiopia, 2022. A community-based cross-sectional study was conducted in East Ethiopia from April 15 to June 11, 2022. Multi-stage sampling was used, and data were collected through structured interviews. Child nutrition indicators were processed using WHO Anthro software. Binary logistic regression analysis was performed, calculating both crude and adjusted odds ratios to assess associations. Variables with a P value <0.05 in multivariable analysis were deemed statistically significant. The study revealed that coexisting malnutrition rates for (OM/SC), (OM/WC), and (OM/UC) were 8.5%, 7.0%, and 7.9% respectively. The double burden of malnutrition among mother-child pairs was found to be 12.3% [95% CI: 10.7, 13.7]. Marital status (divorced) [AOR = 1.80; 95% CI: 1.15, 2.82], child birth order (fourth or above) [AOD = 1.88; 95% CI:1.08, 3.26], number of under-five children in the household (five or more under-five children) [AOR = 1.58; 95% CI: 1.04, 2.39], poor maternal and child dietary diversity score [AOR = 2.76; 95% CI: 1.71, 4.45] and [AOR = 8.66; 95% CI: 4.85, 15.44], respectively, household food security status (food insecurity) [AOR = 3.68; 95% CI: 2.36, 5.75], and maternal stature (short stature) [AOR = 2.39; 95% CI: 1.65,3.45] were factors significantly associated with this burden. The study emphasized the double burden of malnutrition affecting both mothers and children, a major public health concern in the area. Early-life nutrition is vital in preventing childhood under nutrition and adult obesity, leading to this dual burden. Breaking the cycle of malnutrition across generations is crucial. Policy makers should prioritize improving child nutrition and maternal health, stressing early-life nutrition to address the mother-child double burden of malnutrition.