The Malnutrition-Inflammation Score (MIS) was initially proposed to evaluate malnutrition-inflammation complex syndrome (MICS) in end-stage renal disease (ESRD) patients. Although MICS should be routinely evaluated to reduce the hospitalization and mortality rate of ESRD patients, the inconvenience of the MIS might limit its use. Cerebral complications in ESRD, possibly induced by MICS, were previously assessed by using spectral electroencephalography (EEG) via the delta/theta ratio and microstate analysis. Correspondingly, EEG could be used to directly assess MICS in ESRD patients, but the relationships among MICS and these EEG features remain inconclusive. Thus, we aimed to investigate the delta/theta ratio and microstates in ESRD patients with high and low risks of MICS. We also attempted to identify the correlation among the MIS, delta/theta ratio, and microstate parameters, which might clarify their relationships. To achieve these objectives, a total of forty-six ESRD subjects were willingly recruited. We collected their blood samples, MIS, and EEGs after receiving written informed consent. Sixteen women and seven men were allocated to low risk group (MIS ≤ 5, age 57.57 ± 14.88 years). Additionally, high risk group contains 15 women and 8 men (MIS > 5, age 59.13 ± 11.77 years). Here, we discovered that delta/theta ratio (p < 0.041) and most microstate parameters (p < 0.001) were significantly different between subject groups. We also found that the delta/theta ratio was not correlated with MIS but was strongly with the average microstate duration (ρ = 0.708, p < 0.001); hence, we suggested that the average microstate duration might serve as an alternative encephalopathy biomarker. Coincidentally, we noticed positive correlations for most parameters of microstates A and B (0.54 ≤ ρ ≤ 0.68, p < 0.001) and stronger negative correlations for all microstate C parameters (−0.75 ≤ ρ ≤ −0.61, p < 0.001). These findings unveiled a novel EEG biomarker, the MIC index, that could efficiently distinguish ESRD patients at high and low risk of MICS when utilized as a feature in a binary logistic regression model (accuracy of train-test split validation = 1.00). We expected that the average microstate duration and MIC index might potentially contribute to monitor ESRD patients in the future.