This study aimed to investigate changes in time-frequency domain features, complexity, and network connectivity in Alzheimer’s disease (AD) patients following rTMS modulation, as well as to evaluate the relationship between resting-state electroencephalography (EEG) characteristics and Mini-Mental State Examination (MMSE) scores. A total of 15 AD patients were enrolled, and their cognitive status was assessed using the MMSE. EEG features, including time-domain measures, power spectrum, nonlinear dynamics, and graph theory attributes based on phase-locked values, were extracted before and after rTMS modulation. Statistical analyses were conducted to examine differences in EEG features, and multiple linear regression models were established to quantify the correlation with MMSE scores. The results revealed significant improvements in time-domain features, power spectrum, complexity, and graph theory coefficients following rTMS. Additionally, EEG features were significantly correlated with MMSE scores, with an R2 value of 0.321. These findings provide a robust scientific foundation for understanding the physiological mechanisms underlying rTMS modulation in AD patients and for evaluating its clinical efficacy.