Nutritional risk is associated with intensive care unit (ICU) stay and mortality, the Nutritional Risk Screening 2002 (NRS 2002) and the modified Nutritional Risk in the Critically Ill (mNUTRIC) score are assessment instruments and useful in predicting the risk regarding mortality in ICU patients. Our aim was to assess the effects of mNUTRIC and NRS 2002 on mortality in patients on extracorporeal membrane oxygenation (ECMO). A retrospective cohort study was performed and 78 patients were included for final analysis. In the current study, the NRS 2002 and the mNUTRIC score within 24 hours before starting ECMO were applied to assess patients’ nutritional status on ECMO and explore the relationship between nutritional status and patient outcomes. This study suggests that both mNUTRIC and NRS 2002 scores were found to be significant independent risk and prognostic factors for in-hospital and 90 day morality among ECMO patients based on multivariable logistic regression analysis (p < 0.05), with those in the high-risk group having higher in-hospital and 90 day mortality rates than those identified as being at low risk (p < 0.001). In comparison to the NRS 2002 score, the mNUTRIC score demonstrated a superior prognostic ability in ECMO patients.