Ultraviolet-B (UV-B) radiation to thylakoid membrane and fatty acid profile has been investigated in cyanobacterium, Spirulina platensis. The thylakoid membrane was isolated by mechanical disruption of the freeze-dried and lysozyme-treated cells followed by differential density gradient centrifugation and morphological variations were examined. UV radiation distorted the membrane on the outer side with reduced chlorophyll a (chl a) content compared to its untreated counterpart. Liquid chromatography-mass spectrometry (LC-MS) was used for characterization of chl a of the thylakoid membrane. UV-B exposure resulted in alterations in the pigment-protein complexes 47 kDa and 43 kDa. Furthermore, 94 kDa and 20 kDa protein appeared in UV-B-exposed thylakoid membrane of S. platensis. The composition of fatty acid in response to UV-B radiation was detected by gas chromatography-mass spectrometry having 23.5% saturated fatty acid (SFA), 76.4% monounsaturated fatty acid (MUFA), and polyunsaturated fatty acid (PUFA). In contrast to its UV-B-untreated counterpart, SFA was 46.6%, and MUFA and PUFA were 53.3%. Our findings suggest that UV-B radiation not only affects membrane morphology and its protein profile but also reduces saturated fatty acid and increases unsaturated fatty acids in S. platensis.