Objective To explore the correlation between cognitive function and proton magnetic resonance spectroscopy in basal ganglia and thalamus in patients with bipolar depression and suicidal ideation, and to provide reference for clinical treatment of bipolar depression and suicidal ideation. Methods Clinical data of 40 patients with bipolar depression admitted to People's Hospital of Xinjiang Uygur Autonomous Region from October 2021 to May 2022 were retrospectively analyzed, according to whether accompanied by suicidal ideation, they were divided into group A (without suicidal ideation) and group B (with suicidal ideation), with 20 cases in each group. The hamilton depression scale-24 (HAMD-24), hamilton anxiety scale (HAMA), Young's mania rating scale (YMRS), montreal cognitive assessment (MoCA) score were compared between the two groups, the values of N-acetylaspartate (NAA), creatine (Cr), choline (Cho), myo inositol (MI) and lactic acid (Lac) in basal ganglia and thalamus were detected by magnetic resonance imaging, the correlation between cognitive function and NAA/Cr, Cho/Cr, MI/Cr, Lac/Cr values in basal ganglia region and thalamus region was analyzed. Results Compared with group A, HAMD-24, HAMA and YMRS scores significantly increased in group B, while MoCA scores, NAA/Cr value in left basal ganglia, MI/Cr value in right basal ganglia and Cho/Cr value in right thalamus region significantly decreased in group B (all P<0.05). Pearson correlation analysis showed that, MoCA score in patients with bipolar depression was positively correlated with NAA/Cr in the left basal ganglia, MI/Cr in the right basal ganglia and Cho/Cr in the right thalamus (all P<0.05). Conclusion Patients with bipolar depression and suicidal ideation have obvious symptoms of depression, anxiety and mania, as well as cognitive function, neuron dysfunction exists in both basal ganglia and thalamus, and the patients have suffered serious basal ganglia damage, which is associated with cognitive function to some extent, therefore, cognitive function assessment and magnetic resonance imaging examination can be conducted in early clinical stage, to detect suicidal ideation in patients and reduce the risk of poor prognosis.