Mud crab, Scylla serrata, is an important commercial crustacean living in estuarine waters. Studies on fatty acids composition changes in muscle and cell membrane of S. serrata under low temperature adaptation play an important role in understanding physiological adaptation at low temperature. In this study, S. serrata were forced to experience 3week adaptation at different low temperatures. Biochemistry methods were used to determine the content of various fatty acids in muscle as well as cell membrane. For muscle, compared with 27 ℃, C16:0 decreased gradually with the decrease of temperature, and decreased significantly at 5 ℃ (P<0.05); while C18:0 increased significantly at 5 ℃(P<0.05)；C20:5 increased gradually with the decrease of temperature, and was significantly higher at 5 ℃ and 10 ℃(P<0.05).∑C16 decreased gradually with the decrease of temperature, and decreased significantly at 5 ℃(P<0.01);∑C20 increased gradually with the decrease of temperature, and increased significantly at 5 ℃ and 10 ℃(P<0.05). EPA+DHA increased gradually with the increase of temperature, and increased significantly at 5 ℃ and 10 ℃ (P<0.05), while EPA/DHA increased significantly only at 5 ℃(P<0.01). For cell membrane of muscle, compared with 27 ℃, C18:2 increased significantly under low temperature adaptation (P<0.01,P<0.05), and decreased gradually with the decrease of temperature. C18:1 decreased at low temperature, and decreased significantly at 5 ℃(P<0.05). C18:0 decreased significantly under low temperature adaptation (P<0.01); C20:5 increased under low temperature adaptation, and increased significantly only at 15 ℃(P<0.05). C22:6 decreased at low temperature, and decreased significantly at 5 ℃ and 10 ℃ (P<0.05). C20:1, C20:4 and C20:3 increased under low temperature adaptation, and significantly increased at 5 ℃(P<0.01 or P<0.05). ∑C18 decreased at low temperature; while ∑C20 increased significantly at 5 ℃ (P<0.01). However, ∑C22 decreased at low temperature and only decreased significantly at 10 ℃(P<0.05). Under low temperature adaptation, ∑SFA decreased significantly (P<0.05，P<0.01), while ∑UFA increased significantly(P<0.05，P<0.01), thus ∑SFA/∑UFA decreased significantly (P<0.05,P0.01). Increase of ∑UFA was due to increase of ∑PUFAω6. EPA+DHA had no significant change (P>0.05), but EPA/DHA increased significantly only at 5 ℃ (P<0.05). In conclusion, changes of fatty acid composition in muscle and muscle cell membrane of S. serrata are dynamic during low temperature adaptation, in which desaturation, lengthening and transformation happened continuously in short chain fatty acids. Compared with muscle tissue, fatty acids changes in cell membrane are much more, and its saturated index decreased significantly at low temperature. Changes of fatty acids in cell membrane indicated that cell membrane played an important role in maintaining the physiological homostasis under low temperature condition.