Background/Aims: Although abnormalities of amplitude of low-frequency fluctuations (ALFF) and hormone levels of hypothalamus-pituitary-thyroid axis have been reported in patients with bipolar disorder (BD), the association between abnormal ALFF and serum thyroid hormone levels remains unknown. Method: A total of 90 patients with unmedicated BD II depression and 100 healthy controls (HCs) underwent resting-state functional magnetic resonance imaging, and then routine band (0.01–0.1 Hz), slow-5 band (0.01–0.027 Hz), and slow-4 band (0.027–0.073 Hz) ALFF analysis were performed. Additionally, serum thyroid hormone levels including free tri-iodothyronine (FT3), total tri-iodothyronine (TT3), free thyroxin (FT4), total thyroxin (TT4), and thyroid-stimulating hormone (TSH) were detected. The correlation between abnormal serum thyroid hormone levels and ALFF values in patients with BD II depression was calculated. Results: Compared with the HCs, patients with BD II depression showed decreased ALFF in bilateral precuneus (PCu)/posterior cingulate cortex (PCC) in routine and slow-4 frequency bands, decreased ALFF in the right PCu, and increased ALFF in the right middle occipital gyrus (MOG) in the slow-5 frequency band. Additionally, patients with BD II depression showed lower TSH level than HCs, and TSH level was positively correlated with ALFF values in the bilateral PCu/PCC in the routine frequency band. Conclusions: These findings suggest that patients with BD II depression display intrinsic activity abnormalities, mainly in the PCu/PCC and MOG, which are associated with specific frequency bands. Moreover, altered intrinsic activity in the PCu/PCC may be related to TSH levels in bipolar II depression.