Patients with chronic partial sleep deprivation (SD) may experience cognitive dysfunction. The purpose of this study is to explore the pathways of electroacupuncture (EA) by observing the changes in brain metabolites before and after EA treatment in patients with chronic partial SD cognitive dysfunction. The research subjects included 26 chronic partial SD cognitive dysfunction patients and 27 healthy subjects. Montreal Cognitive Assessment Scale, Pittsburgh Sleep Quality Index Scale (PSQI), Stanford Sleepiness Scale, Wechsler Memory Scale, Hamilton Anxiety Scale, Hamilton Depression Scale, Stroop paradigm, psychomotor vigilance test, 2-back test task, and mood assessment test were used to assess sleep quality, cognitive function, and emotional state of subjects. Magnetic resonance spectroscopy was used to detect the basal ganglia of the brain, and the characteristics of metabolites of the 2 groups were comprehensively analyzed, and the correlation with clinical cognitive function evaluation indicators was analyzed. Compared with the control group, the Montreal Cognitive Assessment Scale and Wechsler Memory Scale scores of the observation group were reduced before treatment, while the Pittsburgh sleep quality index, Hamilton Anxiety Scale, and Hamilton Depression Scale scores were improved. The completion ability of Stroop, 2-back, and psychomotor vigilance test decreased. The GABA/Cr on the left side of the basal ganglia area increased. "Adjusting Zang-fu and Arousing Spirit" EA can improve the sleep quality and cognitive function of chronic partial sleep deprivation cognitive dysfunction patients, which may be related to regulating the levels of NAA, Cho, and GABA in the basal ganglia.