Background: Pregnancy strongly depends on the health and nutritional status of women. High proportion of pregnant women affected with poor nutrition which leads them to unhealthy and distress condition. Nutritional problem alongside difficulty of ecological exacerbates public health problem. Determining the extent of problems and predicting marked health indicator require extensive studies to improve pregnant women health to reduce maternal in lowland distracts.Objective: This study aimed to determine the magnitude of malnutrition among pregnant women and associated factors in the central rift valley of Ethiopia, 2016. Methods:Community based cross-sectional study design was conducted using quantitative data collection method. Study area was selected using Handy ® GPS system. Systematic sampling was used to select 616 pregnant women. Nutritional status of study participants were identified using MUAC tape, Height and Weight measured using stand standard height and weight digital scale. Blood sample was taken using Hb 301 Microcuvettes and determined hemoglobin level with HemoCue Hb 301® Analyzer. Hb level was adjusted for Altitude and trimesters. The collected data was entered and analyzed by SPPS version 20. Result:The prevalence of malnutrition among pregnant women was 31.8%. MUAC <21 cm had significant association with Hemoglobin <11 g/dl accounted for 42%. MUAC (AOR, 2.39; 95%CI (1.7, 3.5), Height (AOR, 3.55; 95%CI (2.14, 5.87), ANC services dissatisfaction (AOR, 1.66; 95%CI (1.18, 2.34) and utilized family planning method (AOR, 0.55, 95%CI (0.38, 0.81) were factors associated with maternal malnutrition. Moreover, hypertension 3.9%, severe anemia 0.8%, observed edema 1.9%, and reported infections 4.4 were prevalence in the study population. Conclusion:Maternal malnutrition is highly prevalent in the study area. Anemia, short stature, MUAC<21 cm, ANC service dissatisfaction, not utilizing family planning, teen age pregnancy were the most occurring maternal malnutrition. Integrated programs works are needed to feel the gap for women focused intervention specifically for ecological affected districts.