Objective To explore brain magnetic resonance spectroscopy characteristics and their relationship with cognitive impairment in patients with bipolar disorder（ BD） at different clinical stages. Methods A total of 120 patients with BD admitted to the hospital from February 2016 to February 2018 were selected and assigned into stage Ⅱ（ n=28）， stage Ⅲ（ n=47） and stage Ⅳ（ n=45） groups according to their clinical stages. Another 30 healthy individuals were selected as control group. MATRICS consensus cognitive battery （MCCB） was used for all subjects to assess their cognitive function. 1H magnetic resonance spectroscopy（ 1H-MRS） was used to measure BD patients' choline complex（ Cho）， creatine（ Cr） and N-acetylaspartate（ NAA） of frontal lobe， basal ganglia and cerebellum， respectively. The NAA/Cr and Cho/Cr values were calculated， and the relationship between brain biochemical metabolism and cognitive impairment was analyzed. Results （1） With the exception of the scores of the Wechsler Memory Scale（ WMS- Ⅲ）， the scores of other dimensions in BD patients in any stage were lower than those in control group（ P ＜ 0.05）. With the progression of clinical stages， the scores decreased［ stage Ⅳ＜stage Ⅲ ＜ stage Ⅱ（ P＜0.05）］.（ 2） Across the BD patients in different clinical stages， there were no significant differences in the NAA/Cr on the left side of frontal lobe， the Cho/Cr on the left and right sides of frontal lobe， the NAA/Cr on the left and right sides of the basal ganglia， the Cho/Cr on the left side of the basal ganglia， and the NAA/Cr and Cho/Cr on the left and right sides of the cerebellum（ P＞0.05）. The NAA/Cr on the left side of frontal lobe and the Cho/Cr on the right side of basal ganglia in stage Ⅳ group were lower than those in stage Ⅱ group and stage Ⅲ group， with which， the indexes in stage Ⅲ group were lower than those in stage Ⅱ group（ P＜0.05）.（ 3） The NAA/Cr on the left side of frontal lobe and the Cho/Cr on the right side of basal ganglia were positively correlated with the score of Brief Visuospatial Memory Test-Revised （BVMT-R）（ P ＜ 0.05）. Conclusions BD Patients in different stages all suffer from cognitive impairments to some extent， with abnormal brain biochemical metabolism of NAA/Cr on the left side of frontal lobe and Cho/Cr on the right side of basal ganglia that are positively correlated with cognitive function score.