The total lipids of different strains of Porphyra haitanensis in different culture areas were extracted using Bligh-Dyer method after harvesting at different periods. Fatty acids were analyzed quantitatively and qualitatively by gas chromatography coupled with mass spectrometry (GC-MS) after esterification. The results indicated that polyunsaturated fatty acids (PUFA) dominated the highest proportion in the fatty acids composition of Porphyra haitanensis, followed by saturated fatty acids（SFA）in which C16:0 was the main fatty acid accounting for 26%-33% of total lipids, and monounsaturated fatty acids（MUFA）were the lowest, mainly for C18:1(n-9). C20:5(n-3), or EPA, was the highest in PUFA, of which the relative percent of the total fatty acids was 32%~46%. The same strains of Porphyra haitanensis harvested in the different periods, of which the relative percent of C16:0 was decreasing gradually with the increase of harvest times, while in PUFA the percent of EPA was increasing apparently and the C20:4（n-6） was decreasing gradually. The Porphyra haitanensis harvested in the same period in different culture areas showed that PUFA content in the Zhejiang sea area was higher than in the Fujian. As for the different strains of Porphyra haitanensis in the same culture areas, PUFA especially EPA of ZheDong-1 was slightly higher than ShenFu-2 when harvested the first time. No obvious differences were seen in the other periods. This study facilitates the qualification and cultivation of Porphyra haitanensis as well as food development.