Stunting remains a major public health concern in Ethiopia. Government needs to reshape and redesign new interventions to reduce stunting among under-five children. Hence, this study identified the problem according to location and risk factor. This study is a secondary data analysis of the 2016 Ethiopian Demographic and Health Survey. A total of 9588 children aged 0–59 months were included in the study. The spatial and multilevel logistic regression analyses were used to explore spatial heterogeneity and identify individual- and household-level factors associated with stunting and severe stunting. Spatial heterogeneity of stunting and severe stunting was seen across the study setting. Male children (AOR = 1.51, CI 1.16, 1.96); multiple births (AOR = 27.6, CI 10.73, 71.18); older children (AOR = 1.04, CI 1.01, 1.05) and anemic children (AOR = 3.21, CI 2.3, 4.49) were severely stunted at individual-level factors. Children from educated and malnourished mothers (respectively, AOR = 0.18, CI 0.05, 0.71; AOR = 5.35, CI 3.45, 8.32), and from less wealthier mothers (AOR = 5.95, CI 2.58, 13.69) were severely stunted at household-level factors. Giving priority to the hotspot areas of stunting and older and anemic children, multiple births, and maternal undernutrition is important to reduce stunting. Studies are recommended to fill the gaps of this study.