Nutritional status is one of the most important causes of improper physical and mental development in children. The study attempts to assess the factors affecting the severity status of children aged 6–59 months’ malnutrition based on the weight-for-age anthropometric index (z-score) and examine between-kebeles-level differences in determinants of the nutritional status of children. A community-based, cross-sectional study design was conducted from October 12 to November 12, 2022. A sample of 397 children aged 6–59 months primary data by applying multi–stage clustered sampling technique was used by considering their heterogeneity. The data were entered by SPSS and analyzed by using R version 3.4.0 and STATA 14.2 statistical software package using a multilevel ordinal logistic regression model and inferences were conducted at a 5% significance level. The results show that birth interval ≥ 24 months (OR = 1.431253, 95% CI 1.221337 1.6763421, P-value = 0.008), economic status of households medium (OR = 16.21466, 95% CI 1.221403 1.423929, P-value = 0.000), economic status of households rich (OR = 223.2856, 95% CI 1.34295 2.582325, P-value = 0.000), employment status of the mother unemployed (OR = 0.2291348, 95% CI 0.0529511 0.9966281, P-value = 0.049), No toilet facility (bush field) (OR = 0.3163329, 95% CI 0.1825356 0.5481975, P-value = 0.000), number of household members (OR = 0.9100682, 95% CI 0.8313481 0.9967315, P-value = 0.042), breastfeeding < 12 months (OR = 0.53803, 95% CI 0.322315 0.898135, P-value = 0.018), educational level of father Primary (OR = 4.601687, 95% CI 1.758009 2.22053, P-value = 0.000), educational level of father Secondary above (OR = 99.65229, 95% CI 2.533502 4.788896, P-value = 0.000) and geographical area (kebeles) were found to be important factors that affect a child's nutritional status between 6 and 59 months. 15% of the overall variation is attributable to the Kebeles level, according to two-level multilevel ordinal logistic regressions with estimates of the variation attributable to the Kebeles level equal to 0.569 and an intraclass correlation coefficient of 0.15. Due to the nature of the response variable random intercept model with random coefficients fitted the data adequately in predicting the severity status of children aged 6–59 months’ malnutrition for the multilevel ordinal logistic regression model analysis. So, the researcher recommended that implementing primary health care and nutrition programs that would fit each kebeles’ features in Itang Special Woreda to safeguard children from nutritional deficiency.